Pokémon Diamond and Pearl/WMG

This page deals with Wild Mass Guesses for games and species in the Sinnoh region. For non-game and non-Sinnoh game WMGs, please refer to the appropriate page in the Pokemon WMG Index.

Shaymin represents gender equality.
First, look at regular Shaymin. Shy, small, and even girlish. Now, look at its sky form. It has changed from a hedgehog to a deer! It even has antlers, which usually go to the males of a species. It's also obvious how masculine it is. Compare the voices in "Girantina and the Sky Warrior." Shaymin's voice in its regular form sounds feminine, while its sky form sounds tomboyish. Its gained flying type could be a metaphor for freedom! Its weakness against ice can actually stand for criticism.

Spiritomb is not a Pokemon.
Spiritomb is actually many souls of different people bound within a keystone. It may even be a demon. The binding gave it special powers that caused it to be wrongly classified as a Pokemon.
 * But it can breed! Perhaps the people/demon became a Pokemon?

Rotom was going to be a legendary, but Game Freak changed their minds at the last minute.
Hence why the legendary music plays when you fight it.

Cresselia has a Miracle Eye sort of effect that only works on Darkrai.
Psychic vs. Dark... how does she negate his nightmares and hold her own in fights with him in Explorers? She must have some kind of Miracle Eye effect, one she doesn't exploit when with a Trainer, perhaps because of Honor Before Reason.

Kyogre is Manaphy's Biological mother.
The dad could be Lugia or something. Or maybe Kyogre's just magical like that and can lay eggs without any father. Sort of like the whole "Manaphy can only breed Phione but Phione doesn't evolve into Manaphy" sort of thing.
 * Immaculate conception. Arceus is the father. Manaphy is PokeJesus.
 * Or there was a religion based off Kyogre, and Manaphy was their saviour.
 * Or that would make Kyogre the Virgin Mary Pokemon.
 * Manaphy is a special, more powerful than average Phione, that's why they breed but only Phione are made. But maybe Kyogre had something to do with Manaphy's specialness, perhaps it is the result of a Phione it willed to become pregnant as a display of its power?

The Veilstone Myth was Giratina's fall
Giratina is listed as a renegade Pokemon, suggesting that he and Arceus aren't on the best terms. Though the dialogue of the Veilstone Myth is more befitting Shaymin in this troper's opinion, Giratina is a popular pick for it. This was also the end of the golden age where Pokemon lived together with humans. Giratina either hated the age, and simply wanted it gone, or believed the current arrangement was more suitable, but was shot down by Arceus. And so he went over his head. Giratina first planted a powerful sword where someone suitable would find it, leading to the massacre of the region. Once the person repented, he then offered his own setup as a covenant, which was accepted. Arceus certainly didn't like it, but as humanity entered the deal willingly, he was unable to revoke it.

Giratina represents antimatter and regular matter.
Origin Forme is antimatter, and Altered Form is regular matter.
 * See Here.
 * When it's a living shadow, it represents dark matter.

Giratina actually represents the force of gravity.
Palkia represents space, and Diagla represents time. Gravity, according to the Theory of Relativity, is defined by the warping of space-time, which would fit Giratina thematically with the other members of its trio, as well as explaining its space-time warping abilities. In addition, its home "dimension" is most notable for being a place where gravity is all wonky, which fits in with this ability (in essence, Giratina exerts its control over gravity to act as a kind of living black hole, wrapping the fabric of space-time around it to create a "pinched off" area of extremely warped space to use as its "nest" - it can use the same principle on a smaller scale in order to vanish from the physical universe during its Shadow Force attack). Finally, it has two Formes, one which is affected by gravity and one which defies it. Makes a lot more sense than connecting it to antimatter, which doesn't have any of the qualities Giratina is known for.
 * Also, Shadow force, it Giratina leaving the current space and time, which it could do with enough control over gravity.
 * Given the above, Giratina could represent both matter/anti-matter and gravity. After all, what generates the warping of space-time? Matter. This includes anti-matters, since its basically the same as matter except that the particles have a reverse charge. Dark matter may actually be the overlapping of the Distortion World and regular universe.

Giratina shifts into the Reverse/Distortion/Torn World when it uses Shadow Force.
You know, its signature move where it vanishes completely, and then uses an unblockable attack. It fits with its power in the movie, though I'm not sure if it's shown to freely shift between worlds in the games.

Giratina does not represent antimatter, it represents spirit.
The renegade Pokemon banished for its violence? Logically it was either banished to the distortion world and cursed to take on an altered form if it left without permission or it was banished from the distortion world and the altered form is further punishment. Either way it can't inherently represent antimatter since it either is not originally from the distortion world or something equal to or greater than Giratina defeated it inside that place.

Well Cyrus blames the strife that occurs in the world on spirit and seeks to eliminate spirit. Notice that when he gets really close to achieving this goal Giratina shows up to put a stop to it? Why would the renegade Pokemon care what Cyrus does in another world, especially if it's the world it was kicked out of? Because Cyrus was making a direct attack on the thing it represents! When Giratina hatched from the egg Arceus made, living spirit entered the world!

The Arceus you encounter is just an avatar of the real one
You didn't think a god would let you catch it, did you? You just caught its powerful, but not supernaturally powerful, avatar to interact with the real world. The real Arceus is chilling in some dimension making a new avatar for himself.
 * This is just what I thought as well. Clearly, Arceus is nice, and he just wants to make you feel good for catching such a rare Pokemon. But he's also happy he's getting a laugh at your expense...
 * You mean sort of like Umlaut in Xanth?
 * Maybe Arceus was just bored? Or maybe it has to run a Celestial Bureaucracy and got fed up with it. If it needs to escape, it shouldn't be that hard for it to break out (since it happens to be a god).
 * You stopped Cyrus from enslaving its top creations, and presumably fought hard enough for them to consider you worthy of fighting with them. You're rather impressive, for a human. That's why Arceus even considers allowing you to challenge it.

Alternatively, you never actually caught Arceus. The Pokedex is mistaken.
Really, how would it know? What did you catch, then? Not sure, but it was probably a bad idea to do so.
 * You caught a ditto with delusions of grandeur.

It doesn't matter that you caught Arceus, because Arceus's only purpose was to create the world; Dialga, Palkia, and Giratina keep the balance.
And when you catch Dialga, Palkia, and Giratina, Arceus just makes another one. Arceus went to sleep after creating the world, and was never going to wake up. But you were deemed worthy enough to have it join you.

Mewtwo is out to expose Arceus.
This may be a bit of a stretch, but after reading an earlier WMG but it's established from the very first movie that Mewtwo has a resentment towards the humans that created him artificially (although in the English dub, they got rid of the part where he admits to despise the scientists' meddling through creating clones) and had a hatred towards other humans and their Pokemon, because of this. Well, it wasn't just the cloning that peeved him, it was the fact that these humans were trying to make themselves out to be like a God by trying to create life. Think about it; Team Rocket is evil, and Mewtwo knew of their plans. Why would you think they'd want to create an ultimate Pokemon? Clearly, they were trying to create all these powerful beings, like Mewtwo, to have an army of ultimate Pokemon to take over the world with. And what better ego boost is there other than to gloat "I created this army of ultimate Pokemon out of nothing, therefore that makes me God!" However, Mewtwo was just not pleased with that mentality. He was created by science and grew up around it, most likely he would be anti-religious or prefer to take logic over mythical answers.

So, after the events of the first movie, he goes off with all the clones he made to do what exactly? Well, clearly he is doing something, and it has something to do with doing the same with other frauds attempting to build themselves up as Gods. Think of him as the Dark Messiah in this case. With all the new Pokemon coming up each generation, you can't honestly believe that he'd be ignorant of their existence, or of the new legendaries? Not only is he learning of these new legendaries from other Pokemon or from sneaking around in society unnoticed and gaining the information from the humans who know of these legends, but also has decided to find out whether these legends were true.

While researching, he's found out that Arceus, and the other legendaries that are building themselves up into a God-like level, are not really Gods and had no part in creating the word. In fact, this is all a Plan by Arceus to make himself up into a God. He is just an insanely high leveled Pokemon, that clearly would be more stronger than the other wild Pokemon as most of them aren't even allowed over level 50 in the games (other than that place where you get the 100 leveled Magikarp, but then, Magikarp is useless) so in comparison can look to be God-like to them. Arceus could have easily beaten up these weakened Pokemon, to make them all consider him as their God and creator of the world. He then appeared to the humans after coercing the Pokemon, so after giving a show of an extrem4 amount of power, and having the other Pokemon turning into grovelling wimps before him, the humans were under the impression that Arceus must be their God. After a few generations, even the Pokemon began to believe this, and the humans were being fooled into making the legend of Arceus quite disproportionate, so that everyone really did believe that he created the world.

This is where Mewtwo comes in. See, unbeknownst to Arceus, one Pokemon actually had the intelligence to question his authority as God and PROVED IT WRONG. Yes, Mewtwo knows Arceus is a fraud, and is not happy with that! He went to confront this so called "God" to beat the stuffings out of him for deceiving all the Pokemon and humans. Mewtwo's not afraid to blow the enemy up a few times before getting to the explanations, so of course it'd be perfectly in character for him to attack first, getting Arceus before he has time to say "Wait, What?" However, Arceus isn't a push over, oh no. There's a reason why the other Pokemon listened to him and announced him as their God. The two get into a small fight, of epic proportions, but it is stopped shortly as Arceus realizes that Mewtwo isn't just any Pokemon he can deal with by a single "Judgement" attack. So Arceus flees, waiting for the perfect opportunity to strike back. This is why Arceus is impossible to find, because he is hiding from Mewtwo. Mewtwo, on the other hand, is out searching for Arceus to finish off the job, which is exactly what he's been doing all this time and why he seems to prefer spending more time around human civilization rather than staying secluded with only Pokemon. He's trying to find some more reliable sightings of the fraud, as Arceus could easily order the other Pokemon into lying on his behalf, but no human would be able to understand Arceus to obey his order and they would be too shocked when seeing Mewtwo to even think of lying.

Now, this may go on for quite a while; however, Arceus isn't just going to back down. Hell no. He's rounding up the other legendaries to get back at Mewtwo. But with all these powerful Pokemon gathering, it easily caught the attention of others, including Mewtwo. He figures out what may be going on, so it decides to go search for some DNA of the other legendaries, to make clones out of them to help him in the fight if the original legendaries really do decide to help Arceus. So now, Arceus has his army of the real legendaries, while Mewtwo has his own army of clones of the legendaries. When they finally do meet, of course expect a massive battle to happen. This battle will most likely be a future Pokemon movie. The battle will be Epic, it will be Awesome, and most importantly, it will be TV Tropes Made of Win Archive.
 * However, the anime tends towards All Myths Are True, and being born out of and growing up around science is not the same thing as being anti-religion. Particularly in psychic types.

Arceus and Mewtwo are opposites (almost).
Here we go. In the beginning, there was Arceus. Arceus created Mew as an outlet for its power. However, even that was not enough for Arceus. It created the Pokemon World, and its human inhabitants, but it still needed to create. It released all its power to the outskirts of the Pokemon Universe, and began to draw in beings from other planets, fandoms, and mythologies, then channeled them into Mew, who altered them into Pokemon and released them into the World. This would explain why Pokemon tend to look like creatures from Earth, other fandoms, and mythologies. However, Arceus still wasn't done. Over the course of the games, it churned out more and more Pokemon. During the first few years of the Pokemon Universe, scientists cloned Mew, creating Mewtwo. As Mewtwo was a clone of the second most powerful Pokemon in the world, it was unbelievably strong. However, the way it was created (horrific genetic experiments, according to several Pokedexes) caused its power to manifest in the form of negative, destructive energy instead of positive, creative energy, making it a negative double of Mew, and, as such, putting it almost at the level of Arceus. Like Mew (and by extension, Arceus), Mewtwo wanted to create life, but as a negative being, it couldn't create its own life, and it had to clone others the way Mew was cloned to create it. This caused the first movie. Once again, though, because the cloned Pokemon were created artificially through bizarre cloning machines, they released more and more negative energy. Eventually the negative energy began to reach Arceus, who started creating legendary Pokemon to stave it off. However, as Mewtwo and his clones continued to exist, they pumped more and more negative energy into the world. This caused the villains of each series to become progressively more evil, and as the negative energy grew stronger and stronger, Arceus made stronger and stronger legendaries to counter it. Eventually, the negative energy began spilling out of the Pokemon Universe, forming the Torn World and Giratina. Cyrus is almost completely full of negative energy, which drove him insane and made him try to annihilate the world and remake it. Things are beginning to come to a head, and soon Arceus and Mew will have to deal with Mewtwo themselves.

Arceus is not the creator of Sinnoh, but its first conqueror.
The second Plate you pick up in Sinnoh reads "This plate is formed from the power of defeated giants" (or a slightly different wording). Now, why would "the giants" (which obviously refers to the Regis) have to be defeated if they were servants of Arceus? Answer... they weren't its servants until it beat them into submission. The only thing we have to go on for saying that it is a god are some old legends, which are unreliable due to probably being Written By The Winner, and the Pokedex articles, which are unreliable because the Pokedex also contains such blatantly impossible errors as Magcargo being significantly hotter than the freakin' SUN.
 * Lightning is hotter than the sun.
 * Not for as long of a time as Macargo.

Arceus is God In Name Only.
It's true that Arceus created the universe, but that's about it. Arceus is merely what started the cosmos. It's only true divine power is the ability to create, hence the title: the Alpha Pokemon. This is why you, a mere mortal, can capture God-because God turned out to be pretty much a weakling.

Arceus is the Hive Mind of the Unown.
Think about it: in the Johto remakes, you can create a Dialga, Palkia or Giratina egg using Arceus. During the ceremony, Arceus summons a horde of Unown to create an egg. Arceus is more or less the soul of the Unown, made manifest into a Pokemon. The Unown are the actual body. This is why the Unown are useless: they're essentially projecting their entire consciousness into Arceus, making the actual Unown near-mindless. This is also why you can capture Arceus: it has no power on its own, and the Unown can create another focus for their consciousness. Finally, note how the Unown cannot breed whatsoever, despite being neither baby Pokemon or legendary? They really are legendary.
 * Or you got it backwards and the Unown are the unseen thousand arms of Arceus, its tools and or independent parts of Arceus's body, enough mind to function on their own but still under the creator's control.

Cherrim was going to be a Grass/Fire Pokemon, and its ability Flower Gift was meant to raise all stats in Sunny Weather
However, it was found to be so powerful in the alpha/beta testing stage, it was powered down Up to Eleven. It went too well.

Cyrus was the developer of Porygon-Z.
Porygon-Z is created by trading Porygon2 with a Dubious Disk found in the Galactic Headquarters in Veilstone. Porygon2 is created by trading Porygon with an Upgrade that you can find in the Galactic Building in Eterna. In Platinum, a guy in Veilstone offers to give you a Porygon that he found by the Galactic Headquarters.

So, someone in Team Galactic wanted a Porygon, and had the means to upgrade it, and had developed a mod to upgrade it further.

By know-how alone, Cyrus is the most likely candidate, as he's canonly noted to have an affinity for machines and programming and to be extremely intelligent. Emotion has been one of the biggest hurdles to overcome in Artificial Intelligence research, so Cyrus would find Porygon an excellent parallel to his Emotion Suppression philosophies. Lastly, the Porygon-Z mod on the Dubious Disk was meant to upgrade it so it would be able to travel into other dimensions... such as the Distortion World, perhaps? Or maybe just to escape the destruction/recreation of the universe so Cyrus could guarantee himself a powerful Pokemon in the new universe.

Long story short, Cyrus developed the Dubious Disk. The Porygon you got in Platinum was supposed to be his prototype, but he obviously never got it (and then you took the Upgrade and the Dubious Disk, too).

Arceus is did create the world as it is known but is not God or even a god.
After Diamond/Pearl/Platinum came out Heart Gold and Soul Silver confirmed that Arceus is the one who shaped the world. Then Pokemon Black and White came out and said powerful Pokemon are worshiped as gods but really are not? Who is right? They both are. Perhaps Arceus was sent from another universe to shape this one so Pokemon could live in it? Maybe Arceus is a creature born of the primordial chaos that brought order to existence? Maybe it can do things inherently, maybe the hall of origin amplifies its power?

Pokemon, especially legendary ones, have been shown to do great things in cut scenes. Maybe he's beatable by players because Gamefreak cared more about catching and trading than plot. Maybe he's just holding back because Pokemon battles are for sport, not to the death. Pokemon are mysterious beings even to the people in the game, they don't fully understand how they work or where they came from yet(even Porygon is buggy). There is no reason Arceus can't have god-like power but still be subject to the some of the same basic rules of other Pokemon.

Drifloon and Drifblim are demons.
They're ghosts that steal children and take them to the underworld. That sounds like a demon to me. Presumably they take the form of balloons because nobody would take them seriously.
 * They'd take the form of balloons because small children are fascinated by balloons.

Roark is Silver's brother
The new HGSS artwork for Silver depicts him with similar hair to Roark, and since hairstyle is apparently hereditary in the Pokemon world, this means that they share at least one parent. This could possibly mean that Silver's father is actually Byron, and the mention of Giovanni's son having red hair being just a coincidence.
 * Perhaps they're cousins, and Byron's sister married Giovanni. It'd make as much sense as your theory.
 * Or, since Byron is a MANLY MAN and Roark is ...uh... not..., Roark more likely takes after his mom than Byron. This would also explain why Roark's mother/Byron's wife is absent, since Silver is (probably) younger than Roark...
 * If they are brothers, either it's through the same mother or Roark's mom slept around - HeartGold and SoulSilver'' confirm that Silver is, in fact, Giovanni's son.

The Rival from Pokémon Gold and Silver is Roark when he grows up.
Here Either that, or Roark is his real father.
 * Impossible, the Johto and Sinnoh quests are near-simultaneous. And hairstyle does not necessarily imply direct relation.
 * Besides, Roark's father is Byron, and Silver's is Giovanni. Unless... Oh god, I've squicked myself out.

Mars is Silver's older sister, and Ariana is their mother.
Mars. Silver. Ariana.

Coincidence? I think not.
 * Holy crap... Also, to combine this with the previous theory, Roark could be Silver's half-brother.
 * This would also explain why Ariana is the only female Rocket executive.
 * Ariana=Silver in welsh.

Will and Lucian are brothers.
They both are from their league's respectives Elite Fours, have purple hair, use Psychic Pokemon, and dress in an elegant way (although Will's more of a flamboyant/Tuxedo Mask parody). The similarities are there for everybody to see. They could be siblings and, ironically, Lucian would be the older one.

Lt. Surge is Volkner's uncle or older brother.
They look somewhat similar, they have blond hair, they're both Hot-Blooded, and they're both electric fans.
 * I also think of the Gym Leaders in terms like that. Like maybe Candice is Pryce's granddaughter, or Phoebe is Morty's cousin, etc.
 * Wattson is Volkner's grandfather, Lt. Surge is his father/uncle, and Elesa is his cousin.

Byron doesn't age.
He has the energy level of a hyperactive 8-year-old, and is still in pretty damn good shape for a man in his mid-40s. Also, here is an image of him in the series' present day. Here is how he looked in a flashback to roughly 10 years ago.

Cyrus has a run-in with Mesprit before the events of DPPt.
It explains why he is so emotionless and hates it; he no longer has the ability to comprehend emotion and spirit and can only see all the negative aspects of things of that sort.
 * Except then, he wouldn't have emotions at all, rather than just suppressing them. Granted, it's possible he encountered it, but it didn't take his emotions. Unless, of course, he later got them BACK...
 * Well, you do see Cyrus at Lake Verity right at the beginning of the game in Platinum. While obviously he didn't capture Mesprit then, it's possible that it at least messed with his emotions then even if it didn't outright take them all away.

Cyrus is the Omega Pokemon
Arceus, the Alpha Pokemon, is said to be the God of Creation. So the Omega Pokemon would be the God of Destruction. However, it doesn't just come out of nowhere. Cyrus, by some means (Celebi, most likely) travels back in time; to the moment of creation. If he can't destroy the world and recreate it, then he'll go back before the world was even created. He succeeded in gaining the godlike power he desired, but was sealed away by Arceus and its offspring before he could do any significant damage. But soon, he will awaken...
 * How would that work with Cyrus having a living grandfather?
 * Cyrus is the reincarnationm of the Omega Pokemon

Alternatively, Cyrus will become Poke-Satan.
He already shows those qualities, considering his attempt to control the gods, recreate the universe and hatred towards creation itself. At some point, he will learn how to harness the power of the Distortion World. And the War in Heaven shall begin...

Cyrus is Arceus' Satan equivalent.
Cyrus was once a legendary Pokemon who rebelled against Arceus and attempted to take Arceus' power for himself. Present at creation, Cyrus disagreed with many of Arceus' choices, among them choosing to give the gift of spirit to mortals, which he saw as a curse rather than a blessing. He attempted to overthrow Arceus, but failed. Rather than kill him, Arceus chose the worst punishment possible for him: to be made the weakest of Arceus' creations and locked into an eternal cycle of death and reincarnation. While his memory of being a legendary was erased, Cyrus still subconsciously resented Arceus and wanted to correct his mistakes, however it was only in his latest incarnation that he chose to act on it. He gathered a group of followers and attempted to create a new universe, only to be stopped by the intervention of a young trainer and one of Arceus's servants. Cyrus is still out there, however, and he will never stop in his quest to overthrow Arceus.

Cyrus has already gained minimal control over the Distortion World.
You can't go back to the part of the Distortion World you fought him and Giratina in, and thus you never see him again. But WHY can't you go back there? Consider this--the last thing he says to you includes the vow that he'll gain control over that world and become a god from there. Of course, it's not much, but at least you won't be disturbing him while he gains true power.

Cyrus is the Only Sane Man in Sinnoh.
Metaphorically speaking, of course. But he's the only character in game canon to bring attention to or even seem aware of things like warfare and that the world is basically not the sweetness and light place people keep insisting it is. Imagine growing up in a world similar to the real world that you and I all share, only with no one ever talking about the bad things that go on or have gone on or how to prevent them from happening again, choosing instead to play around with cute monsters all day. It's no wonder he felt he had to go to such extreme lengths to change it... or to get anyone to listen to him.
 * On that note, Pokemon were actually bred or built to serve humans in war... and Cyrus is the only one with half a clue!

Cyrus is either an empath or an Aura user.
He's able to sense Giratina's anger before there's any sign that it's present, and he can sense power in both the world and in people. And if he picks up on the emotions of those around him, no WONDER he has such a negative view of them--he's overloaded by every negative emotion anyone could think of!

Mars is from Jubilife and Saturn is from Pastoria.
They represent the traits associated with the spirit of the nearby lakes. Meaning the weak link in the chain is Jupiter--she's not unusually intelligent and her reaction to snow means she wouldn't be from Snowpoint. However...

Cyrus would have kept Jupiter in his world, but not Mars.
Saturn is already eliminated from the equation. But Mars... Cyrus even refers to her as the "bringer of war", owing both to her name and her violence, and both war and emotion are things he's trying to eliminate. Jupiter, not embodying any of the traits of the lake spirits, would be more malleable in his reshaping the population of his new world.

The Ribbon Syndicate is part of a conspiracy to control Sinnoh.
Sounds crazy, right? But think about it for a moment. No matter where you are in the game, even if you've beaten the Elite Four and captured Arceus himself, the suspiciously grandiose building in the Resort Zone won't let you in unless you have 10 or more ribbons. Who's to say this Ribbon Syndicate isn't looking to recruit powerful trainers with lots of ribbons, in the same way the Church of Happyology wants to recruit powerful people? And according to Bulbapedia, the spa treatment this Syndicate provides includes diamond and pearl dust as part of the treatment.

Now how exactly would a lowly ribbon club get that kind of money? And what, exactly, are they using it for? To hire ex-Team Galactic goons to shake down people for protection money? Who's to say?

Maylene's mother died, and her father is neglectful.
When Maylene comes to visit your villa, she comments that he comes to watch her train only after he wins at the game corner. Clearly, Maylene's mother died at some point in her childhood, and her father turned to a life of gambling to cope with it. He gets so engrossed with gambling, however, that he ignores his own daughter most of the time.
 * Alternatively, Maylene's mother ran away and broke her father's heart, so he became so depressed he took to gambling.

Maylene is in cahoots with Team Galactic.
Not a full time member, but Lucas/Dawn's Pokédex DOES get stolen by Team Galactic as soon as you beat her. She must have called them right before you challenge her/right after you beat her. Also explains why the headquarters is right in the same city, but she never acknowledges its existance.
 * Alternatively, Galactic owns the casino where her father apparently spends most of his time. They won't let her father go home until Maylene sells you out to Galactic. This is why her father speaks about her so fondly, even though he's 'neglectful'.

Maylene is poor.
Her father is always seen in the Game Corner, and excessive gambling is not a very good career choice. She also always seems excited at the idea of free food, as seen in the battleground and the restaurant in Celadon City. She never uses potions in battle (as opposed to other Gym Leaders who use them ALL THE FRICKING TIME), which gives the implication that she can't afford them.
 * Maybe she can't afford shoes either?
 * And just think - after defeating her, you, the player, took away half of her remaining money. What the Hell, Hero??
 * Not quite; payouts are now determined by the trainer's highest-leveled mon, plus, for the player, their badge count.

Gen IV's bag stores items as data.
Hence why it has an infinite space.

Cynthia really is a pedophile.
Johto, Sinnoh, and Isshu? Meeting random kids 'randomly'? Even if she is going there for plot reasons, it seems unusual.
 * Technically, the Isshu guys are teenagers. And in Johto and Isshu, you've kinda got to go looking for her yourself.
 * Teens still aren't legal. Do we even have confirmation on Iris's age?(Or Hilbert/Hilda's?)
 * Yeah, but Johto and Isshu is just sightseeing. She and Dawn are actually together, and she's not going to cheat on her (especially since the girl controls four godlike beings).

Cynthia is a huge Professor Rowan fangirl.
She starts being nice to you as soon as she sees you got the Pokédex from Professor Rowan. And she's always mentioning stuff about helping out your Pokédex. She tells you to say hi to him after your first meeting, too (which you don't do, ya jerk).

Cynthia is a Chansey.
I know this sounds completely insane, but think about it. Remember that one myth in Canalave's library that talks about a Pokémon that turned into a human? I posit that said Pokémon is, in fact, Cynthia. She mysteriously demonstrates the ability to heal your party to full just by holding them (with the Pokémon Center noise, might I add,) after the Distortion World, not to mention the magic egg full of "happiness" and the Secret Potion for the Psyducks. Not only that, but she frequently pops out of tall grass to speak with you, has an egg charm on her jacket, and has those... head... doodlebobbers- all rather reminiscent of the common Chansey, wouldn't you say? I rest my case.
 * A few counterpoints:
 * 1) Cynthia has family members older than her. Plus, that book's pretty old.
 * 2) Other people can heal your Pokemon, like every one of the stat trainer partners, and Cheren and N in Black and White.
 * 3) That egg is a Togepi egg. She has a Togekiss. Do the math.
 * 4) Secret Potion comes from Cianwood. Game even says so.
 * 5) That's not an "egg charm"; for one thing, it looks more like a teardrop.
 * 6) Her hairclips look more like Lucario's aura-sensors (with an Umbreon color scheme).

Cynthia is a former player character.
Think about it. She says several times that she also went on an adventure with a Pokedex when she was younger. And she's Sinnoh's champion, which is a position that the player character always ends up holding.
 * I'd say that your mom in Black and White is one, too. She says herself she used to be a Trainer, in any case.

The unused Red Chain item in Diamond and Pearl was going to summon Dialga in Pearl and Palkia in Diamond.
In Diamond and Pearl's coding, there's item data for the Red Chain. It seems unlikely that the player would bring about Dialga or Palkia, so they had Cyrus do it instead, and had it planned so it would be used to obtain Palkia or Dialga in the opposite version.

Fantina is Canadian
It avoids any (major, her brokenish English/French in the French and English versions would be odd, but not plot effecting) Dub Induced Plot Hole as she speaks French and/or English depending on the translation. The 2nd best option (French that lived/studied/traveled/preformed/whatever the UK/got taught English in school), though isn't quite as clean with the "avoid confusion for any country" move (why does she exclusively use English in the Japanese version?).

The Pokemon Mansion in Sinnoh holds a very, very dark secret.
The Master Liam of the 5-Maid Knockout Exact-Turn Challenge will tell you that you don't need to know what's going on in the back of the mansion, but he winks at you at the same time. What's supposed to be going on with a master and 5 maids in the back of a mansion? I don't really want to know. Maybe they're having some sort of party, or baking a cake?

Professor Rowan is a reincarnation of The Therearah.
Name's the Same and all.

Cyrus is The Antichrist...
To Giratina's Satan. Unknown to Cyrus, Giratina manipulated aspects of his life so that one day it could be freed from the Distortion World. Cyrus had no clue, and believed he was remaking everything. Only when Dialga and Palkia were under control, could Giratina finally be free. You capturing Giratina? Pah...Giratina allowed that. Giratina has lived eons, while you are but a mortal. You released the Pokedevil, and have no comprehension of what you've done. The world shall fall, the stars shall die, and the renegade will reign...

Cyrus will escape from the Distortion World, but will either die or suffer a Fate Worse Than Death shortly thereafter.
Think about it: he could spend years in the Distortion World, without food or water or even a regular sleep schedule. If he ever bothers to leave, that could catch up to him, to say nothing of the people who might pounce on him the second he returned to civilization. On the other hand, it's possible that Uxie, Mesprit, and Azelf placed curses on him, and those curses will take effect the second he leaves.

Cyrus is an illegitimate child.
If one of his parents wasn't his biological parent that might have lead to his abuse when he was young. And a contributing factor to his distrust of emotions may be that he doesn't want to fall in love and risk creating another illegitimate child to suffer the same way he has.

Cyrus is an Evil Counterpart to Volkner.
Think about it: they're both highly-intelligent Gadgeteer Geniuses who spent a portion of their lives in Sunyshore, they're both powerful Pokemon trainers, they're both withdrawn and depressed for various reasons, and then there's the renewable energy focus of both of them (Cyrus's Team Galactic researches alternative energies as a cover, and Volkner likes solar panels, one of the most famous renewable energy sources to date). Cyrus's name is derived from a word meaning "sun," the star at the center of the solar system; and Volkner's title as per his gym is "The shining, shocking star." Hell, they even look something alike!

Maylene is on friendly terms with Cyrus, or at least thinks of them as such.
She'd be much more likely to let someone she already knew build up his shady business in her own city. If she considered Cyrus her "friend," then her lack of concern about Team Galactic despite their being almost literally at her doorstep makes sense. And if you consider that even most of Cyrus's own followers seem to think he's an honest, reasonable man, he wouldn't have to do much to make friends with a young girl who's got tremendous power but not much experience, and already has a lot on her plate with her Gym Leader responsibilities and neglectful father.

Maylene and Candice are lesbians.
They did seem rather close, and it would be pretty cute.

Maylene is a The Woobie (not my explanation)
Maylene is a gym leader in Veilstone City. It's also suggested that she's remarkably young for the role, lauded as the 'barefoot fighting genius'. The truth is, the city of Veilstone is using her. Gym battles, naturally, bring a lot of revenue in for a city...And given Maylene's strict, disciplined lifestyle, she doesn't seem to use very much of that money on herself. Her father is an obsessive gambler. He spends virtually all of his free time in the city's Gamecorner, tossing away his daughter's money. Even when he manages to win, his greed and obsessive nature only causes him to eventually waste every ounce of cash that he receives. All the while, he and the entire city encourage Maylene to continue on track...Tirelessly training. Her youth makes her a novelty...just one of the many sites to see on any tourist's journey to Sinnoh. She's afraid of disappointing the city she grew up in as well as the only family she has...so instead of mingling with people her own age, she trains and trains and trains. The only real 'friend' her own age is Candice, the gym leader of Snow Point. At one point in the game, she goes to visit Candice in Snow Point. She walks the entire way...barefoot. She explains that she could just use a Flying-type to make it there quickly...but she never uses any Flying-type Pokemon, so it's likely that it was a lie. She insists that the journey is for training...But in reality, she simply can't afford any other way of making it to Snowpoint other than walking on her own. Crasher Wake sometimes visits her...and once, he actually took her all the way to Celadon City. She was thrilled to see the eating contest there...since it was the only way she could actually eat until she was full considering her vow of poverty. Secretly, she wishes Crasher Wake was her father...and though he's offered to take her away from it all, she resists temptation to remain loyal to her father and city.
 * Well, yeah. You could make the case that just about anyone in this game is The Woobie, unless said character was happy all the time to begin with (maybe not even then).