The Legend of Zelda: Skyward Sword/WMG

Guesses from about what would be in the game before the game was released has been moved to a separate page:
 * The Legend of Zelda Skyward Sword

The Grand Unified Keese-Feces Insane Theory
We didn't get the full backstory. In addition to Hylia, there were two other deities set to protect the Triforce. One embodied courage and one embodied power. The minor goddess of power's story was lost to history, but not completely: it is still known that she had red hair and golden eyes, and many desert civilizations worship her as the Desert Colossus. The minor god of courage's name was also lost to history. He is now known as the Fierce Deity. The Colossus was most likely one of the first divine casualties, but she managed to pass on some minuscule part of her into a human bloodline. This bloodline eventually bore Groose, then the Gerudo. The Fierce Deity's story, though, is more interesting. He was wounded, unprepared, by a sneak attack by the mad demon Majora and her high priest, known only by his rictus grin, chilling laugh, and ability to pull large musical instruments from the ether. Knowing that if he died, his power could be used by the demons, he asked Hylia for help. He needed some way to keep his power safe from the forces of evil without eradicating it altogether. Hylia, by this time, was already formulating a plan to become mortal and use the Triforce. She took out her harp and played the Song of Healing. The Fierce Deity's spirit -- the part that contained his power -- filtered into another human bloodline. His soul -- the part that made him who he was -- was sealed inside a mask, which eventually fell into Majora's hands, but could not be used to its full extent, as it did not contain the power. Link never remembers who he is because he does not have that soul, only the spirit, whereas had both. didn't tell him because that would be a stupid idea -- we've already seen what happens when a body of demonic origin attempts to form without its consciousness. The same situation, but of divine origin, would likely be worse. So when the Hero of Time put on that mask, he knew, just for a few minutes, what was really going on. It helps to explain why he looked how he did in Twilight Princess.
 * But the Fierce Deity's mask was implied to be evil.
 * Majora said that. Besides, it all depends on how you define "evil." Majora's Mask dealt with the theme of moral ambiguity a lot, especially towards the end.

Link is still left handed
The Knight Academy just trains all the pupils to use a sword right handed regardless of dominance. Link still uses his bow left handed. Seeing as he had to figure it out himself he would instinctivley revert to being left handed.
 * Technically, how one holds a bow is based on eye dominance, not hand dominance. Link's just right eye dominant, and therefore holds his bow in his left hand. Furthermore, right eye dominance is more common than left eye dominance, so Link is already more likely to hold his bow in his left hand.

The City in the Sky is Skyloft
This is obvious, but less so is where do Ooccoo and her ilk come from? Inbreeding. Eons of inbreeding.
 * More likely, some Skyloftians brought some "tiny birds" back up to the clouds for use as pets, in much the same way we look upon very small dogs. Eventually, the humans all moved to the surface. Evolution and residual magic stemming from the physical presence of a major goddess for 15 years or so and of the Triforce for just a few moments did the rest.

Alternate to above, the Cloud Tops in Minish Cap were a part of Skyloft
As in, this should be Fanon by now. The game that officially follows SS is TMC.

Both The City in the Sky and Cloud Tops were part of Skyloft
Darn place covered all of Hyrule, there's more than enough of it for the remnants to form the basis of multiple mini-cities later on. The Oooccoo were just squatters, and the Cloud Tops people were explicitly recent immigrants ingame.

Lanayru Desert Regrows
Think about it. Compared to the TP map, which is basically an updated, more realistic version of Oo T's map, Lanayru desert looks exactly like what would be Hyrule Field. Of course, the sand sea and a small part of the desert likely stays the same— thus creating Gerudo Desert and the Haunted Wasteland. I suppose the temple of time could become Hyrule Castle Town and Hyrule Castle, with the master sword being relocated there for the events of Oo T. Since Demise's essence is sealed inside the blade, that probably explains why it has time-traveling abilities... he, according to Fi, "conquered time itself..."

And the sealed grounds are the actual temple of time, seen as the forest temple in oot, and the temple of time in tp.

Your red loftwing will reincarnate in the future as Epona.
Think about it, other than being an Expy, Epona and Link share a special connection, just as he and his loftwing do. The reason they are connected is because they somehow sensed this on a subconscious level that they are destined companions.
 * Well in Nausicaa of the Valley of the Wind, the giant birds evolved from horses, maybe the opposite happens here?

Gannondorf was possessed by
Rather then Ganondorf being a, Gannondorf is actually merely being possessed by him. Given there are multiple Links and Zeldas but only one Ganondorf there is no real indication he is capable of reincarnation himself.

Based off of this I figure his Ganon form is taking a more direct role in the conflict, and the fact that he is permanently in this form in pre OOT games (Which occur later in the timeline) can be attributed to  deciding to do away with Ganondorfs human form so that he can directly act.

With windwaker the two might have been separated, in the opening we see the events that led to the flooding of Hyrule, but the figure we see terrorizing Hyrule is rather demonic looking, whereas in game Ganondorf is far more human then his other appearances and I believe this is the only game he does not have a beast like form. This would serve to explain Ganondorf's rather sympathetic characterization, not knowing he was possessed he would have tried to justify his actions to himself claiming he wanted to help his people escape the harsh desert, despite his actions in OOT not suggesting this as the gerudo never actually leave the desert despite ganondorf ruling Hyrule. Not possible. was killed, and his consciousness was sealed in the Master Sword. Possession requires a consciousness.
 * Actually there's a minimum of two Ganondorfs, considering that Ocarina of Time and Four Swords Adventures give him separate origin stories.
 * IIRC,  especifically stated that an incarnation of his hatred would appear to carry on his war against all the Zeldas and Links for eternity. So while Ganondorf is most definitely not   or being controlled by him, he's certainly subconsciously influenced by him.

Groose's Bloodline got Shafted
In the conflict four human characters play prominent roles, Impa who has a legacy of Impa's that take care of Zelda. Zelda, who has a legacy of Zelda's who have the Triforce of Wisdom. Link who has a legacy of Link's who have the Triforce of Courage and can wield the Master Sword. And Groose, who's lineage is never heard from again.

If someone who's heart is not in perfect balance gets the Triforce, they only get one piece and the other two find their destined bearers. Ganondorf was not chosen by the Gods to get the Triforce of Power he just stole it, and then the other two pieces sought out Link and Zelda. But what if Ganondorf valued Wisdom or Courage above Power? Perhaps Groose's bloodline would've been chosen to inherit The Triforce of Power in the event one of the other two was taken by someone unworthy, but instead Ganondorf,  stole his.
 * Don't worry. Groose's descendant got his day in the limelight. He became a legendary hero, married another spunky blonde princess, mastered another form of timeshifting, and defeated another giant abomination covered in spines. (Unfortunately, it didn't turn out so well for Groose's native sky islands - but hey, you can't make an omelette without breaking a few eggs.)

Gaepora is Kaepora Gaebora, but not Rauru
Gaepora is Zelda's father. Zelda is the Seventh Sage. So, rather than being Rauru, Kaepora Gaebora must be an ancient Seventh Sage!
 * Gaepora isn't the father of the Zelda that was the Seventh Sage. He's the father of

The demons that invaded the land are bosses in later games.
More specifically, Ganon, Dethl, Bellum, Malladus, Majora, Onox, and Veran.
 * I believe Malladus is a new reincarnation of 's hatred, as they're both given the title of Demon King, and in the timeline Malladus appears in, Ganondorf has been killed, but  's curse lasts for all time.

The City in the Sky was a part of Skyloft.
Seems too obvious to not be so, the Palace of Winds from The Minish Cap may be connected too.

The graphics are this way because of a Xanatos Gambit on the part of Nintendo's PR Department(s)
They're trying to prove beyond a shadow of a doubt that the Zelda's overprotective fans are 100% unpleasable. In fact, since this game can be found in both They Changed It, Now It Sucks and It's the Same, Now It Sucks, I'd say they've succeeded.
 * Please, that was the 1% of the fans that can't shut up and let the 99% enjoy the game.

This Link is the Hero's Shade, not the Hero of Time
The armor he has is ''really' old looking. Much older than the style seen on the guards and enemies in OoT.
 * Jossed. He's the Hero of Legend.
 * Errr... sorry, how is that jossed then? Just because he's the Hero of Legend in this game doesn't mean he can't be the ghostly being referred to as the Hero's Shade in Twilight Princess...
 * One problem with this: The Gamecube version of TP is canon, which means the Hero's Spirit is canonically left-handed. SS Link is right-handed.
 * Jossed by Hyrule Historia, which explicitly states that he's the Hero of Time.

Possible titles for this Link.

 * Hero of (the) Sky
 * Hero of Skies?
 * Hero of the Master Sword
 * Master of the Sword? Eh?
 * Hero of Hylia
 * Hero of the Goddess
 * Hero of Legend
 * Sidekick of Groose
 * Hero of Rebirth (in multiple ways -- he helped to give law back to the surface,, and he was the original Link in the cycle of rebirth.)
 * The First Hero
 * That's unlikely, as the introduction states that Hylia did have another hero before him, during the war that led to the creation of Skyloft. However, nothing suggests that the hero was a Link.
 * The First Link in the Chain, perhaps?

As mentioned before in the main Zelda WMG, the legend of Zelda is real and remnants of it still remain.
My proof? This Video of Fi walking about Fresno California without a care in the world!

The clothes the Hero of Time wears as an adult actually belong to this Link.
In Ocarina of Time, when Link wakes upas an adult, he finds that he's been given new (adult-sized) clothes that still have a Kokiri style, with no explanation whatsoever. In the E3 2011 trailer, a man with a striking resemblance to Rauru (the Sage of Light in Oot) can be seen... giving SS! Link his trademark green clothes.
 * Alternatively, the clothes that Ocarina Link wears are just bigger versions of the Kokiri clothes he's used to, and the clothes that SS Link wears later become the Hero's Clothes in Twilight Princess. They are identical, down to the embroidery on the tunic and the chainmail.
 * It says in the manual for OoT that the Kokiri tunic is "One Size Fits All". Clothes changing would be pointless, he just got bigger in his One Size Fits All tunic.
 * That outfit (at least in Skyward Sword) is supposed to be the Skyloft Knight academy outfit in Link's year's color. For example, you meet a character who is stated to have graduated last year, with the same outfit... but in yellow.

The Birds from Skyloft are the origin of the Hylian Shield's design
Self-explanatory.

The islands in the sky are in fact the islands from the Wind Waker.
Just compare the Skyloft island where Link lives, and the layout looks very similar to Windfall Island. It also stands to reason that the gods flooded Hyrule because they knew civilization could find and take refuge on the islands that were always there.
 * That's an awfully large height for water to get to....
 * Two Words: Colony Drop.

The flying in this game got it's inception with the flying in Twilight Princess.
When Nintendo was working on the flying minigame parts of TP, they probably got the idea that "hey, why don't we make this the main mode of transportation in the same manner as the horse and boat?" Thus, they took notes from how the flying worked in that game and how it worked in Wii Sports Resort and came up with the flying in Skyward Sword.
 * It also could've been based on the Fluzzard segments from Super Mario Galaxy 2, since both of them involve diving in order to gain speed. The only difference is that Link's loftwing can flap its wings to gain altitude, while Fluzzard can only glide.

Fi is Fee
FEEE!
 * Fee, Fi, Foe, Fum...

The Happy Mask Salesman is one of the old Demon Lords
There's a figure directly to the left of the demon leader in the prologue that looks suspiciously similar to the Mask Salesman. Explains his creepy nature, his immunity to time, his desire to retrieve Majora's Mask, which may very well have been his leader and his subsequent disappearance afterwards.
 * It's also worth noting that the demon lord to the left of said silhouette appears to be wearing a mask.
 * And Chancellor Cole is his descendant.
 * I think Cole is a Lokomo, though.
 * Alternately, the Demon Majora was somehow exorcised, its power collected into a mask, leaving behind a human figure which became the Mask Salesman.

This game leads right into

 * Although considering how the timeline works, it leads right into Zelda II by a few thousand years.
 * Eh, don't think so because

Link is a reincarnation of

 * Zelda mentions that ; in the same way that a reincarnation of, this fanfic (not written by me) raises the possibility of Link being the reincarnation of.
 * Or, due to the Timey-Wimey Ball, the story of is actually the story of.
 * I support this theory. Possible supporting facts is the Time Wimey Ball; since Impa  is the originator of the Impas who protect the Zeldas , it could have been perfectly possible for her to spread these stories in the past to take shape in the future, essentially giving the legend Zelda tells an air of Self-Fulfilling Prophecy when seen in hindsight.
 * To expand upon this,
 * Wait...you don't mean...

Batreaux

 * Once he becomes human
 * In addition if you look at the symbol on the floor of his house and turn it ninety degrees it highly resembles the Gerudo symbol, Batreaux looks like a muscular redhead when human and as a demon had much in common with the Snes Ganon. Both with an affinity for bats, skull decor, blue skin and pig like faces.

Demise's
Normally.

Groose is related to Kemo's hair

 * Just look at his hair! Can't you picture him saying "Attention Link! My hair definitely did not hide your Loftwing in a cave behind the waterfall!
 * Those child-grabbing classes were worth every penny!
 * Alternatively, Groose's descendents include both Kemo and Gaston.

Groose is an ancestor of the Gerudo, or even Ganondorf himself
He's got the hair color down. And he has Eyes of Gold like Ganondorf. It's not unreasonable that generations of descendants would acquire the darker skintone if they settled in a desert region. It's possible Groose eventually helped found a civilization that would become the Gerudo. Perhaps even becoming the great great great grandfather of Ganondorf or something. His name DOES sound similar to Gerudo (unless I'm mispronouncing one or both names) and he did joke about naming something after himself when he first came to the surface.
 * One of the bugs is called "Gerudo Dragonfly", meaning that "Gerudo" does not derive from "Groose".
 * But besides that, we don't hear another mention of "Gerudo." Gerudo could have lived there at one point before Skyward Sword, but right now it seems unlikely, even with the dragonfly. That, and I kind of doubt Groose's similar appearance to the Gerudo/Ganondorf is entirely coincidental. Red hair/gold eyes is an unusual combination.
 * What's more, during the few cutscenes after, Link is positioned in a very distinctive three-person formation with two other people. When he enters the sealed temple for the last time, he looks for a moment at Impa (on his left), and Groose (on his right), all of whom then turn to face the door to Zelda's room. This formation repeats itself during  , when Zelda comes toward Impa and recognizes her Bracelet. Groose is in the back, looking confusedly at Zelda as she approached. Link is on his left, closer to Impa. Zelda is on his opposite side, approaching the happy reunion. In this way, Groose is positioned in the place reserved for the bearer of the Triforce of Power, along with Link the Bearer of Courage and Zelda the Bearer of Wisdom.

Groose is an ancestor of Malon.
They both have red hair. Well, it makes just as much sense as him being the ancestor of the Gerudos.

The original Legend of Zelda takes place immediately after Skyward Sword.
Because the surface world doesn't have any towns or large settlements of people yet. It also dovetails nicely with Skyward Sword being released on the 25th anniversary of the series.
 * But the original Legend of Zelda's Hyrule already had towns, a royal family, and atleast centuries of history; they just weren't in the physical game itself. It's immediate sequel had buttloads of towns.
 * Not to mention.
 * Jossed by the new official timeline.

Link is a Time Lord... But not any Time Lord, he's The Master
Fi knows the truth, and for that reason addresses him for his more well-known name. This also explains why he's apparently the only thing not affected by

The Ancient Robots were built by the Dark Interlopers
Their imprisonment in the Twilight Realm wasn't part of the civil war in Oo T's backstory, but a different, much earlier conflict that resulted in a fertile region in the west of Hyrule being blasted into the desert we know and love. Their robots continued their civilization for a while, but ultimately fell into ruins while their erstwhile masters were stuck in another dimension mutating into the Twili. Or maybe the Dark Interlopers were just inspired by the robot-makers' art style. At any rate, there's some obvious aesthetic connection there: compare this, this and this to this, this, and this, respectively.
 * That could explain why the Dark Interlopers tried to steal the Triforce in the first place, they wanted to used its power to restore their destroyed environment. That could explain why the Twili, while dark in nature and banished by the gods for serious crimes, are often an example of Dark Is Not Evil: their act of stealing the Triforce wasn't a race of Evil Sorcerers trying to pull off an A God Am I out of pure selfishness but an act of desperation to save the dying people of a once powerful and noble Magitek empire.
 * It might also lend some credence to the theory that the Dark Interlopers were originally Sheikah (both races have a strong connection to shadows/darkness), since what appears to be the Sheikah "Eye" is found on the Timeshift Stones.
 * It's worthy of note that Twilight Princess states that the events that led to the Dark Interlopers' banishment were the very first attempt to steal the Triforce and that they were stopped by Faron, Eldin and Lanaryu. These are the names of the Light Spirits in TP (Ordona appears to be a lesser Spirit), but they're also the names of the three guardian dragons in ''Skyward Sword" (Perhaps the dragons were killed in the vast span of time between the games to return as the Spirits? 2 of the 3 have very dragon-like forms.), so that would certainly match up between the stories. Lastly, the Arbiter's Grounds, where the Twili were first banished, and the Lanaryu desert, where the dead civilization lived, are in the same region, as can be seen in a comparison of maps of Hyrule from TP and SS.
 * Also worthy of note is that its stated that they tried to steal it by breaking into the Sacred Realm- meaning that as of Skyward Sword, they haven't done so yet, as the Sacred Realm is either not created yet or not used yet, and won't for a few generations at least. Perhaps they become desperate enough to try only when the Timeshift Stones run out?
 * Alternatively, it could have been the ancestors of the Oocca, who claim to have originally lived on the ground in Twilight Princess. After they depleted the terrestrial world's resources, they decided to leave for the City in the Sky so that the other races would work to restore the land below, leaving their machines behind.

Demise didn't just
curse specifically mentioned, but who's to say that was all that happened? The backstory of Majoras Mask notes how alternate worlds such as Termina came into being when the Goddesses created Hyrule, and the residual bits and pieces slipped through the cracks of creation and coalesced into separate realms. So it's possible that
 * Guesses as to
 * Or they all represent his Hatred, as the other villains really only come to prominence in times and places where Ganondorf can't rear his head.
 * Or they all represent his Hatred, as the other villains really only come to prominence in times and places where Ganondorf can't rear his head.
 * Or they all represent his Hatred, as the other villains really only come to prominence in times and places where Ganondorf can't rear his head.
 * Or they all represent his Hatred, as the other villains really only come to prominence in times and places where Ganondorf can't rear his head.
 * Or they all represent his Hatred, as the other villains really only come to prominence in times and places where Ganondorf can't rear his head.

Alternatively, Demise caused every villain to exist.
Or at least their plans to a degree.
 * We already know that
 * Bellum:
 * Malladus:
 * Majora:
 * Vaati:

Everyone in Skyloft is convinced Link is a narcoleptic
Which is why they don't question it when he randomly falls asleep in their beds. The denizens who visit the Lumpy Pumpkin have told the owner about it, which is why he doesn't say anything when Link falls asleep in his bed as well. Beedle is the only person who doesn't know of this, but he doesn't really mind when Link sleeps in his airship anyway.
 * The people in Skyloft aren't just convinced that Link is a narcoleptic, Link is a narcoleptic. This explains why Zelda calls him "sleepy head" and why he almost falls asleep when sitting in chairs.

The Silent Realm becomes the Sacred Realm. Its also not a spiritual test for Link.
Think about it. It's a realm where the Triforce is kept. The Guardians are there to protect the Triforce. The entrance gate protects any who enter as giving them a last chance to escape. The Tears of the Goddesses are needed to gain access to special treasures, but since the Goddess's chosen hero needs to enter the Silent Realm, they are given the bonus effect of pausing the the Guardian security system. The reason the security system is turned back on after 90 seconds is just in case the tear was picked up by anyone who entered the Silent Realm other than the Goddess's chosen hero. That's also why the Guardians confiscate the tears when they stop you, so they'll be there for the Goddess's chosen hero. The Watchers and the Waking Water are back up systems to turn on the Guardians should an intruder be able to collect the tears. This also explains why in Ocarina of Time, behind the door of time in the Temple of Time, it looks like an ordinary chamber, but in truth, it is the Silent/Sacred Realm, since the Silent Realm looks exactly like the surroundings of the area you enter into the Silent Realm from.
 * Take note of how the Silent Realm is entirely blue, just like the Temple of Light.
 * Additionally, upon

The Sword that is not destroyed.
It didn't actually fade away with the Big Bad; it was actually just teleported to safety in the farthest reaches of the Desert of Doubt. There, it gets reforged

Ganon turns the Guardians into the Darknuts.
Assuming the "Silent Realm is Sacred Realm" thing above is true, it is possible that when Ganondorf got into the Sacred Realm in Ocarina of Time, he also had to evade the Guardians to get the Triforce. After doing so, he realized that beings such as the Guardians would make powerful soldiers, so he used his new powers to draw them out of the Sacred Realm and implement them into his army. Unfortunately, because he only got part of the Triforce, the Guardians themselves only retained part of their power. Hence, the Darknuts are strong enough to give Link trouble, but not invincible.
 * That's a cool idea, but unfortunately it's Jossed by the official timeline. There are Darknuts in The Minish Cap, which takes place before OoT.

The Master Sword
The Pedestal of Time isn't just a lock, it's an inhibitor. While the Sword lies within it, 's influence is small, only able to slightly manipulate things, create potential evils. When it's removed from its pedestal by the Hero of the age, be it the Hero of the Winds, the Hero of Time, the The Hero of Light or any other Hero, however, things seem to go from bad to worse. The Hero of Time The Hero of Winds   and while the Hero of Light

So, in the end, while the Master Sword is indeed the Blade of Evil's Bane and the favorite weapon of the Hero, it gained a completely unintended purpose:



Some of Fi's Captain Obvious moments have an explanation.
Whenever you complete a puzzle, you get a cutscene showing the results of what you just did. However, it would be weird for Link to have an out-of-body experience every time he solves a puzzle, so instead, Fi fills him in on what happened Behind the Black from Link's perspective. It's just redundant to us as players because we saw the same thing she did.

Faron got disciplined by the goddesses between this game and Twilight Princess.
While she was busy  She is also the only one of the dragons to give Link another test after he already passed each and every test that her bosses, the goddesses, put in front of him. Not something you want to do when it's only a matter of time before. Clearly she has control issues that need to be sorted out. I wouldn't be surprised if Farore herself turned her into a monkey as a way of humbling her so that she'd be more helpful to the hero next time around.
 * Also, Faron got herself a chaperone. Remember Ordona?
 * Thank goodness someone else also has their gripes with Faron. I thought I was alone!

The Gust Bellows doesn't just provide a gust of wind: it also sprays the Hylian equivilent of Lysol (or some other various aerosol based cleaning agents corrosive enough to flat out destroy grime.)
Explain to me how else all of that dust and sand Link sweeps away using the Gust Bellows just suddenly disappears.

The reason Scrapper is such a jerk to Link is because a previous incarnation of Link caused him trouble.
Link didn't do anything to Scrapper to warrant the hostility he shows towards him, and Link is also the only person Scrapper goes out of his way to insult. Word of God said that while this game is currently the earliest one to date, they didn't say it was the first one. Recall that in Ocarina of Time, Guru-Guru was actually pretty nice before Link played the Song of Storms and messed up his windmill. Perhaps a previous Link did something similar to Scrapper, as he often orders Link to stay out of his way while he's lifting something.

== The Amber Relics scattered across Hyrule's overworld are made out of the material for   == Both of the materials seem to have the same luster and colour as each other.

The Sealed Temple becomes the new Temple of Time.
Meanwhile, the old Temple of Time in Lanayru Desert, gets built up into the Spirit Temple.

The Kokiri Sword used to be
After the beating it took, the sword lost all of its magic and degenerated into the small and pathetic Kokiri Sword. However, when Zubora and Gabora in Majora's Mask upgrade it into the Gilded Sword, it begins to show signs of the powerful sword it used to be (diamond patterns on blade, red markings on hilt, pointy guard shaped vaguely like bat wings, etc.)

Tentalus and Scaldera were residents banished from the Monster World
Scaldera was an ancestor of Mike Wazowski and Tentalus was an ancestor of Celia and this woman:
 * Alternately, Tentalus is the long-lost mutated child gone rogue of Mike and Celia, as they were a couple in the movie.

The Kikwi eventually evolve into the Kokiri, and the Parella evolve into the Zoras.
Which makes the Kokiri Plant People.
 * Its also possible that, being forest spirits, they just change shape on the whims of the Spirit Tree, like they did when they changed into Koroks.

Alternatively, the Kikwi evolve into the Deku Scrubs.

 * Or not, as there are already Deku Scrubs in Skyward Sword.
 * Actually, they don't appear at all in Skyward Sword. It's the Octoroks that have taken in their role, so the theory still stands.

There will be a game that takes place immediately after Skyward Sword.
There are a number of gaps, holes, and other lingering questions by the end of the game. Some of them look like they'll take a while to get resolved, but some of them immediately involve Link and those he knows and thus require a game that will star this same Link. Some of the lingering plot points, in order of immediacy, are  Perhaps also the invention of bombs, as we see that all subsequent Links don't need to look for Bomb Flowers for their detonation needs. And the invention of the Boomerang. Similarly...
 * Actually, the Triforce didn't latch themselves to people until Ganondorf stole the Triforce the first time in Ocarina. When Link reforms the Triforce in Skyward Sword, he's seen with the entirety of it on his wrist, not just the Triforce of Courage. Sure, it's the first he sees on the back of his hand, but he eventually receives all of it. The reason it stayed together under his use is the same reason that it split when Ganondorf used it - the Triforce can only stay together while being used if the user is pure of heart. Ganondorf, using it for his own evil gain, splits the triangles, the (possibly) first time the Triforce has granted an evil wish. That is what caused the pieces to retreat to other indivuduals. The most likely explanation for their attachment to Link and Zelda is

This is not the first Zelda game in the timeline.
I forgot where, but there was mention of this Link not being the first one, nor is Zelda. In addition to the WMG above guessing that Scrapper worked with a previous Link, there will most certainly be a game about the war between Hylia and Demise as described at the beginning of the game. As the Ancient Robots were counted among one of the races that fought during the war, this will be set during the time that Lanayru was verdant and colorful, and the Ancient Robots had not yet been deactivated.

The "cloud barrier" is...
...a layer of supersaturated air several miles thick. Thus explaining why inanimate objects can make it through just fine while still allowing for its function as a barrier: any living thing that went through would drown before coming out the other side.
 * Jossed. When Link uses the Triforce, he falls through the clouds just fine.
 * Not necessarily. As you said, he uses the Triforce, an extremely powerful magical artifact blessed by the goddesses. If it can protect him from the impact that would naturally occur when a floating island suddenly falls from the sky (as I recall, the island's momentum is slowed near the end so it can fit neatly into the pit), it would probably protect him against some other issues as well. Can't have the chosen hero meeting an early death due to something silly like the laws of physics!

The sealed form of Demise is a connection to Ganon
Stating the obvious yes but I'll go deeper. The sealed Demise is weaker than Demise himself right so think about it often(when Ganondorf is involved) Ganon is unleashed when Ganondorf is defeated and thus weakened.

Groose is the ancestor of at least one of Tetra's pirates
For one thing, their themes sound surprisingly similar. Also, it seems that Groose has become one of the closest friends Link and Zelda have apart from each other; his descendents probably were among the royal attendants who are implied to be the predecessors of Tetra's crew.
 * Gonzo is probably the most likely of the bunch to be his descendent; it certainly would create a nice thematic and familial connection between Groose and his Groosenator and Alfonzo and his train.

Demise wasn’t the first enemy of Hylia.
After the Golden Goddesses left the world they had created, but long before the rise of Demise’s armies, several gods tried to seize the ultimate power. They would have used it to conquer, annihilate or purify the heavens. One by one, they perished at the blade of Her Grace, the skilled guardian of the triforce. However, and just like Demise would later promise an incarnation of his hatred, each passing god left a trace of its own. Ironically, one of Hylia’s opponents, known only as the Fierce Deity, was the very source of the “spirit of the hero” the goddess would then manipulate into serving her plans.

Hylia's first Hero was named Mattas.
Fi's Simlish is not random. If you listen carefully, the same "words" show up in relation to English words. The most prominent of these is "Mattas" for "Link". Her calling him that is her acknowledging his role as The Hero.
 * Addendum: Mattas was like Hylia, a deity. A fierce deity.
 * But Fi usually calls Link "Master Link" or "Master" a lot more than just using his name . Maybe "mattas" is hylian for "master".
 * Debatable. "Mattas" corresponds to "Link," but "Master Link" is linked with "Ma'i-Mattas." This normally wouldn't be that important, but the two "Mattas" clips are different from each other. Mattas by itself has the accent on the second syllable, but the Mattas in Ma'i-Mattas has the same stress on both syllables. This was intentional. Most likely, "master (name)" in ancient Hylian is "Ma'i-(name) and "Link" is just how the (common?) Hylian name "Mattas" is translated.

The empty space in the Triforce symbol represents Hylia.
She had no part in creating the land or the Triforce, but stayed on as guardian. Like the hollow "triangle" in the center connects the other three together, she preserves the creation of the Goddesses.
 * Or, alternately, like with the real-world "Yin-Yang", the empty space could represent "Negative Space", or a balancing mechanism, it could even represent the darkness that Demise himself represents.

Hylia's power is the Light Force.
The Legend in The Minish Cap was inacurate, the Minish didn't bring the Light Force, they made the Hylians aware of Zelda's sacred abilities, which also explains why Ezlo, a sage of the minish didn't even know what exactly it was. The rest is self explanatory.

Strich did the whole "use potions to become stronger/more confident" thing long before Fledge tried it.
He's the most physically imposing student at the academy, even more so than Groose. He's also the bravest; note that he is the only knight in training who isn't a part of the Goddess's quest to routinely leave Skyloft, and he's the only resident of Skyloft who dared to enter the thunderhead in its current state. This points to a particularly brave personality and an impressive physical regiment, and considering he's an unskilled enough flyer to not be an upperclassman yet, he probably didn't get it through years of effort at the academy. And he's got both things necessary to obtain a healthy potion supply: expendable funds (he barely hesitates to buy from you at night) and a large bug collection.

The Goddess Sword.
It's stated in-game that Hylia created both Fi and the Master/Goddess Sword to guide the chosen hero. And based on the overall design of Demise's sword, I don't think it's unreasonable to suggest that the two are related somehow. So here's my theory. Hylia forged a number of powerful magical swords to use in the war against Demise. During the war, Demise seized one and corrupted it, forming the Dark Master Sword. Hylia was forced to seal them all away, but she knew it wouldn't last, so she created Fi (perhaps she was inspired by ) and went on with her Plan for when Demise escaped. The other magical swords were lost to time, but they retained some of their power. One of them was found by the Minish and given to the Hero of Men, but it was broken by Vaati and reforged with the power of the elements to become the Four Sword. The Lokomo Sword was found by nondescript "Spirits of Good" and given to the Lokomo (who gave it to Link), the Great Fairy's Sword ended up in Termina, and perhaps the White/Magical Swords (from the original) and the Kokiri Sword (from Oo T) might be related too. This is a comparatively weak WMG, but I just like the idea.

Skyward Sword split the timeline. Again.
At the end of the game,
 * Alternatively, the entire game is a stable timeloop, as evidenced by
 * Just one thing, given that the game is a timeloop, then how can the ?
 * But if, why does The Imprisoned exist in the present? Unless
 * But if, why does The Imprisoned exist in the present? Unless

The three dragons are not the same characters as the three Light Spirits from Twilight Princess
It's possible that the names of the provinces came first, and then those names were given to actual people. So, the dragons and the Spirits took their names from the provinces, but are otherwise unrelated.
 * Alternativley Faron, Eldin and Lanaryu aren't names, but titles given to the gaurdian of said region.

Loftwings that learn the Spiral Charge technique are capable of traveling to and from the surface of the world at will.
Something about being able to pierce the heavens, I suspect.

Eldin is somehow related to Volvagia.
Either he IS Volvagia, or Volvagia is his offspring.
 * Regardless of which is true, this means that Ganondorf's actions in Ocarina most likely corrupted all of the Dragons. When the Hero of Time defeated Ganon, they were "reborn" into their spiritual forms seen in Twilight Princess.

Demise is not only the source of all evil in the Zeldaverse, his influence is felt in others.
Consider: the man looks like a Fusion Dance of Twilight Princess' Ganondorf, Nosferatu Zodd, Akuma, and Berserker. As this game is a prequel, he clearly imprinted on many other universes, establishing a foothold there so he can conquer them later.

The timeline split again, and in one of the timelines, Hyrule becomes the Sacred Realm mentioned in the rest of the games.
In the timeline in which most of the game takes place, Demise is completely eradicated by the Triforce, and Link, Zelda, and all the humans and other races watch over the Triforce in peace (Timeline 1, or T-1). In the timeline accessed through the Gate of Time, Link faces Ghirahim and the fully resurrected Demise, and Demise curses Hyrule to face an incarnation of his hatred, who would come to be known as Ganon (Timeline 2, or T-2).

So in T-1, let's assume that Demise was never fully resurrected and never made his curse, and that the Triforce never has to be sealed away because evil has been pretty much eradicated. It follows that this Hyrule becomes a golden land blessed by the presence of the whole Triforce completely controlled by the forces of good. This blessed Hyrule becomes the Sacred Realm.

But in T-2, with Demise having been sealed in the Master Sword but not fully destroyed, and with Demise's curse, evil still lurks across the land, leading to the wars for the Triforce first mentioned in A Link to The Past. But while the backstory states elsewhere that the Triforce in T-2 was sealed away, what might have actually happened is that the Seven Sages actually wished for the Triforce to be beyond the reach of evil, which was fulfilled by having the T-2 Triforce eradicated. Thus, by the time of Ocarina of Time, there is only a single Triforce across all timelines that exist by then.

Thus, the Temple of Time seen in Ocarina of Time does not actually access an entirely different dimension, but simply lets anyone using the Gate of Time access T-2. So when Ganondorf goes through to the Sacred Realm when Hero of Time Link gets the Master Sword, he is going to the Hyrule that was free from evil until he came. As a result, the golden Hyrule of T-1 is conquered by evil once again, and the Triforce is stolen.

The reason the Dark World is Hyrule's dark mirror is not because Ganon's dark heart turned it into that purely by magic, but because it was already Hyrule in another timeline. Because T-1 Hyrule was an evil-free utopia, there was no need to maintain any sort of army, meaning that Ganondorf conquered it rather easily. Certain gloomy aspects of the Dark World may stem more directly from the natural effects of being a subjugated realm.

As a result of all this, the split timelines that Word of God has officially confirmed (Adult timeline, Child timeline, Decline timeline) split off directly from T-2. However, T-1 gets split alongside it because the Sacred Realm/Dark World is confirmed to exist in all of them and gets affected differently each time as a result. In essence, there are actually eight timeline splits: the two from Skyward Sword, and the three pairs of splits for those previous two from Ocarina of Time.

On a side note, this might also result in two other effects regarding the two swords that are central to the plot of Skyward Sword.

For one thing, the Master Sword of T-1 does not contain the lingering essence of Demise. It's possible that, because it is completely free from any evil, it becomes the ultra-powerful Golden Sword from A Link to the Past. This would explain why it is found in the Dark World/Sacred Realm/T-1 Hyrule. And the reason it is found in the possession of the Great Fairy Venus rather than in a pedestal is because, during Ganondorf's invasion of the Sacred Realm/T-1 Hyrule, the forces of good took the T-1 Master Sword/Golden Sword from its pedestal and hid it before Ganondorf could find it and destroy it.

Also, as speculated above, Ghirahim does indeed become the Trident of Power. The Ghirahim of T-1 goes through the Gate of Time to T-2, revives Demise, gets forcibly turned into the Anti-Master Sword, and is eradicated when Link defeats Demise. However, the Ghirahim of T-2 would still exist; it's just that Demise being locked in the Master Sword would mean that his evil machinations would unfold quite differently from how they did throughout Skyward Sword.

First, because the resurrection of Demise is no longer a goal that T-2 Ghirahim can attain, his efforts instead focus on either conquering Hyrule himself or making sure Demise's curse is brought about. It's possible that Ghirahim became the founder and leader of the Dark Interlopers who tried to steal the T-2 Triforce and eventually became the Twili of Twilight Princess. This would explain certain similarities between the Twili characters and Ghirahim (similar Villain Teleportation, strange skin coloring, over-the-top mannerisms, ultimately subservient to the vastly more powerful Demise/Ganon). In fact, when Midna talks about the ancient king who was driven mad by the same greed that she sees in Zant's eyes, she may have been referring to T-2 Ghirahim.

But due to the failure of Ghirahim's Dark Interloper plot, he falls back on Plan B: seal himself in the Trident of Power and make sure that, in this form, he can help the eventual incarnation of Demise's hatred attain the height of his magical potential. In fact, Ghirahim may have either created or influenced the development of the Gerudo to make this flow more smoothly. For one, he influenced their culture so that they would wish to isolate themselves from the other inhabitants of Hyrule, making them extra protective of their desert land and all dwelling in it, including the Trident of Power's resting place. Also, he altered their biology so that there would only be one male Gerudo every 100 years, ensuring that, among this pet race of Ghirahim's, there would be a convenient vessel for Demise's curse who would be in a position of sufficient power (King of the Gerudo) to amass an army and be on high-enough diplomatic ground with the Royal Family of Hyrule to manipulate them. Twinrova may have been a colleague of Ghirahim's who made sure all this came to pass.

The Hyrulean Civil War resulted in multiple genocides.
Skyward Sword introduces the Kikwis, the Mogmas, and the Parellas, which, being a prequel, means these races must somehow cease to exist by the time of the later games. Of what little we know regarding the Hyrulean Civil War, there is mention of the Zoras and Gorons being enemies at the time. We know that Gorons and Mogmas both existed in the time of Skyward Sword, and presumably, had some overlap in territory. While the Zoras were not present, it seems more likely that they shared a habitat with the Parellas than that they evolved from them. So, it is possible that the war could have killed off most if not all of the Mogmas and Parellas. As for the Kikwi, there are multiple possibilities, none of which stand out as most likely. One is that they were magically transformed into the Kokiri. Another is that they died from either destruction of their habitat, or their own stupidity by having their entire species get stuck up in a tree. Lastly, it is possible they could simply have been hiding this whole time, and just not have been relevant.
 * "Must cease to exist"? No, it just means they aren't around. Hyrule has never equaled the whole world in any of the games.
 * The evolution possibility is not so unlikely. Both the Zora and Kokiri were shown to be evolving races throughout the series already (differently from, say, the Goron, who never change). In the Parella/Zora case, it seems like a move from boneless solely aquatic beings to more humanoid and amphibious beings would be a step forward. In the Kikwi/Kokiri case, the Deku Tree's children were always more like spirits of the forest than an actual race, and the Kikwi being weird animal/plant hybrids seems to fit well with that (specially since the Korok are also like that).

Gratitude Crystals only appear to one who knows about them.
This is why they can't be gathered before the meeting with Batreaux, and why they aren't seen in any other games.
 * So it's sort of like Tulpa theory?

Levias is somehow connected to Ordona
It's just as powerful as the three dragons and knows part of the Song of the Hero as they do, and like them is the guardian of a particular region, the sky, and specifically Skyloft. When the Triforce is taken from Skyloft and Demise is destroyed it makes sense Levias would no longer be needed to protect it, so he came to guard another part of Hyrule. Furthermore, Ordona Province is stated to not be a true part of Hyrule, and Levias is an outsider to the three dragons since it is a separate creature.

Just like Fi does, Ghirahim gives frequent tips and tutorials
The only difference being, rather than robotically churning out statistics with everything like Fi, instead his tips, tutorials, and Captain Obvious moments are filled with innuendos (particularly when it comes to thrusting and stabbing) and vaguely Tsundere complaining whenever  uses another weapon.
 * There isn't really any evidence of this, but the mental image is absolutely hilarious.

Fi has the same sort of powers as, she is simply forbidden to use them in the context of this game.
Since Hylia planned for Link to grow into a hero of surpassing power, wisdom, and courage, Helping Would Be Killstealing from Fi's perspective; even in bleak situations, she is restricted from physically aiding Link, instead giving him the information he needs to get the job done himself.

Fi .

 * it certainly explains Navi...

The 'Unidentified Beta Enemy' from Twilight Princess was recycled as The Imprisoned.
. That face is hard to mistake.

The Goddess Crest is based on Fi.
and
 * I think it's a mix of that and the Loftwing theory. Although I definitely see the similarity.
 * I think it's more likely that both are true to a certain extent. So, the Goddess Crest may be based on a Loftwing (obvious when looking at the complete crest, as used by the Royal Family in later games) and Fi's cape itself (as well as the Master Sword's guard) might be based on a bird's wing.

In the final battle, Link doesn't actually kill
Rather, he just re-seals him. After all, how many times is the guy blown to smithereens over the course of the game? He can't actually die, only be sealed, until the Triforce is used to break that particular rule. Killing him hard enough to re-seal simply takes a bit more effort when he's restored to full power.

The Timeshift Stones will have some rather scary effects on undead enemies in future games.
Imagine Link has to go through some Big Boo's Haunt dungeon that is filled with Stalfos and other skeletal monsters. Timeshift Stones can be found in certain rooms, and when activated, they cause the Stalfos to regain their flesh. This could have two possible results: a) hostile Stalfos revert back to non-hostile humans who are aghast at the undead monstrosities that they have become, or b) the Stalfos only regain some of their former flesh, turning into the even more dangerous Redeads. The former would make good material for a Player Punch, while the latter would lead to interesting possibilities for dungeon navigation strategies, in that the player would have to switch the Timeshift Stones on and off while accounting for the Stalfos turning into Redeads and vice versa.

Ghirahim is the reason Fi has no arms.
Fi may have had a form as Ghirahim does. It's not hard to imagine him utilizing and chopping her arms off in that more fragile state, perhaps during the Dark Ages before the game takes place. Or it could have happened in a

Demise's curse was broken at the end of Wind Waker.
Daphnes' wish broke the curse. This is supported by the fact that Ganondorf has yet to reincarnate on that timeline.
 * Yet, a new Demon King appeared about a century later... Demise's curse was never about Ganondorf, but about new Demon Kings in general.

Rupin is an ancestor of the Happy Mask Salesman.
Yup.

Demise is a time-travelling Ganondorf.
I seem to remember that Fi's scan on Demise mentioned that he was a "Master of time" or something like that. A quick leap of logic, and here's my theory: After countless defeats by Link, Ganondorf figures out to travel back in time. He travels back in time to before Link was around, becomes known as Demise, and promptly gets defeated by Link. Then, he gets unsealed by Girahim, killed by link, and curses Link, therefore bringing himself into existence.

Ghirahim is a human spirit that didn't rest in peace.
Going with the idea that Ghirahim and Fi are basically counterparts with certain opposite aspects. Fi and Ghirahim were both originally soldiers in the Hylia VS War. That's when Fi lost her arms. When Fi died, Hylia resurrected her and gave her the task of aiding Link, and put her in the sword. in response, did the same to Ghirahim, except his task is to resurrect if he should die. Fi finished her task of aiding the Hero and could rest in peace, and was Ghirahim  So basically Ghirahim and Fi both did their job, and both got to rest in peace. This would explain Ghirahim's creepy smile when It's because he's finally free.

The reason
So Link


 * Alternately,

Fledge has Klinefelter's syndrome
My only rationale for this is that Fledge has huge hips combined with narrow shoulders in comparison. Sure, he's feminine, but his hips are massively large, to the point of being extremely feminine.

The Skyview and Earth Springs are the Wind and Earth Temples in Wind Waker
When I realised the Master Sword looks like the depowered Master Sword in Wind Waker, this theory makes sense. In Wind Waker, the Earth and Wind Temples are where you power up the Master Sword. Why would they it be powered up there? If they were the springs in SS, that would make them sacred to Hylia, who is long forgotten in the time of Wind Waker. But then you realise.

Ghirahim is responsible for/creates Dark Link
How could a magical shadow possibly survive the evil-repelling might of the Master Sword? Well, what if Dark Link doesn't just have a Cool Sword of his own, but is really just the created puppet of that dread blade...

The Fates of the Three Dragon.
The three dragons, Eldin, Faron, and Lanayru have very different personalities, and live in different locations. First, we have Faron, self-centered, thinking much more highly of herself than anyone else, and also probably not as smart as she thinks she is (nice job killing all the monsters in the woods there, Faron, oh wait), Lanayru, who seems to have a jovial nature, playing games with Link even as, as well as having, or at least letting, the robots over mine Lanayru and turn it into a desert wasteland, and Eldin, reclusive, and serious.


 * Of the three, it's not entirely impossible to see Lanayru dying off. Lanayru desert probably eventually becomes the Gerudo Desert of Ocarina of Time. Lanayru, the most carefree and, yes, careless of the three might have been killed (we know they can die as we think of it, even if they technically keep some consciousness) as the hostile Gerudo population moved into the region, or perhaps even from carelessness (he'd already be dead if it weren't for Link's time traveling shenanigans.


 * Faron also sustained serious injuries, and Link saved her. While the woods are typically a more livable area in Zelda games than the desert, Faron could have been done in either by her own self-importance, or even displeased the goddesses when she forced Link to take her own test, after he had passed the others. Her reckless behavior could have also led to the goddesses replacing her with better guardians, such as the Deku Tree, or Jabu-Jabu/Jabun. Another possibility, however, is that Faron eventually begat the original Zoras. The Parellas treat her like a queen, and Zoras typically have a monarchical government. Her scale grants the ability to swim, something only seen from Zoras up until now. In addition to this, take a look at the "Tadtones," compared to some newly hatched Zoras from Majora's Mask. Of course, if her descendants are Zoras, or she helped the Parellas evolve into the Zoras, that still doesn't explain where she is.


 * Finally, we have Eldin. He's the only one of the three dragons in the game which we never have to save from mortal danger, and who actually proves he can handle himself. He lives in a volcano which probably becomes Death Mountain, and unlike Lanayru Desert, the only indigenous population we ever see in volcanic areas are either beasts who he could handle himself against, or the Gorons, who are, well... The Gorons. He's very reclusive, which could have led to him surviving longer, as almost nothing ventures into Death Mountain to kill him. We see two other dragon who live in volcanos in the Zelda series, Volvalgia, and Valoo. Now Volvagia I don't really have a good explanation for, except that he could have been one of Eldin's children who turned evil for... Some reason? And then we have Valoo. Valoo is implied to be very old (he speaks old Hylian), and he has a similar fit of rage causing volcanic activity on the island to Eldin's during Skyward Sword. There exists a serious possibility that Eldin was living inside the same volcano for several thousand years.

Demise Reincarnated as Ganondorf so He Could Use the Triforce
Only mortals can wield the Triforce, that is why Hylia had to reincarnate as Zelda in order to use it. Demise wanted to use the sacred power for himself, but chances are he couldn't use it because he is also a god. This left him in a huge disadvantage in Skyward Sword. As Ganondorf, Demise could use the Triforce just as well as Zelda and Link can.