Yu-Gi-Oh! GX/WMG

Darkness and Zorc are related.
They look alike, they have similar motives, they both use realtively innocent hosts who (using season 0 for Bakura) attract many girls, they each disappear in the thirdish season (Waking the Dragons and Yubel) and reappear as main villan as the forth, they each have two hosts (Thief King Bakura and Little Bakura for Zorc, Fujiwara and Fubuki for Darkness). They're each epic and this trooper is a fangirl of Zorc and thinks Darkness is cute.
 * I always thought that Darkness was the Antichrist to Zorc's Satan. A more human embodiment of the evil shadow demon thing.
 * It is dark. You are likely to be eaten by a grue. Seriously, this is a WMG? It's painfully obvious from the allusion in the names.

GX takes place in a world where the Roman Empire never fell.
The goal of the Princeton borhers is to dominate the economy, politics and dueling. People focus on this gigantic case of Arson, Murder, and Jaywalking, but forget another thing - how the hell do you "dominate" the economy? In the current system, there's no way. Ditto politics - even if you became president of the dominant global superpower (which he isn't because noone ever calls him president). Even if you dominated dueling, its impossible to dominate economics and politics.

However, in the days of the Romans, such goals were easily obtainable. Some businessmen could amass fortunes so large they dwarfed the treasury of the empire, and became the ruler of business, with nothing progressing without their say so. Ditto politics - with no bribery laws, one could thus make their will the dominant force in politics.

This in turn leads us to why dueling is so important - it has taken the place of the Gladiatorial bouts - one of the most important things to the roman people, something that genuinely was on par of importance with the economy or politics.

The Abandoned Dorm incident was a semi-failed attempt to recreate the Egyptian God Cards and Millennium Items.
The original Millennium Items needed 99 human souls to be created, and while the exact number of students missing was never established, it's big enough to force a cover-up. Also, note that the Shadow Charms bear some resemblance to their Millennium Item counterparts (for instance, the Millennium Eye and Shadow Eyepatch), each with an unspecified power. Then, there's the similarity in both look and effect/strength of the Sacred Beast Cards and the Egyptian Gods; and dueling energy is needed to reacquire them. (The Egyptian Gods and Millennium Puzzle required a duel for them to legally change hands; the Sacred Beasts need all seven Spirit Keys to be won by a challenger in a duel to unlock their hiding place). Finally, replicas of the hieroglyphs that were required to unlock Pharaoh Atem's memory (also using the Items and Egyptian Gods) are on display at the Abandoned Dorm, and there's a hidden dueling arena in a cave underneath the Dorm. This all seems to point to an attempt by Kagemaru to recreate the Millennium Items and Egyptian God Cards. It only worked in part; the lack of demonstration of the Shadow Charms' powers indicates that they - like the Sacred Beasts - aren't as powerful as the originals.

Star Wars episodes 4 through 6 were one of the inspirations for some of the show
Think about it. Judai is kind of like Luke Skywalker, and  went from Darth Vader (because of  ) to Obi-Wan Kenobi because of   And   is somewhat like Emperor Palpatine, because both were

Yubel was supposed to be the Supreme King.
The first person Jaden dueled in the Dark World was Harpie's Brother, who told him to beware the Supreme King. But since  is supposed to be the Supreme King, Harpie's Brother shouldn't have ever heard of the Supreme King. Then later, Ojama Yellow reports seeing Jesse, only he "looked kinda weird", aka he had the Supreme King's golden eyes. Since Jesse was supposed to be, it doesn't make sense for him to have golden eyes. Also, when the Supreme King first appeared in  mind, it is just a shadow that then transforms into the Haou   look. It's likely that  was actually possessed or mind controlled by Yubel into becoming the , instead of it being inside his head the whole time. The story was probably changed at some point to give him more angst and to wrap up the season.

Johan Anderson is the half-brother of Yuki Judai and Marufuji Shō/Marufuji Ryo.
Johan's look, personality, and dueling strategy are all similar to Judai's, but he has teal hair and some physical characteristics like Sho and/or Ryo. Plus, we know nothing about Johan: not his age, not who his parents are, nothing. And. Plus, we know that. Sho seems to stay at the Academy with Judai during the holidays, possibly indicating the same, giving their parents enough time to have an affair and keep Johan's existence a secret until they could give the baby up for adoption. Finally, there's Johan's and Judai's feeling that they met somewhere before their initial meeting; close relatives do seem to have a knack for sensing when their siblings are near. They also have a Ho Yay Love Triangle going, so this could lead to some... interesting developments once the truth comes out.
 * Alternatively, Johan is Yubel's amnesiac good side given its own life. Again, both Johan and Judai think they know each other from somewhere before their first meeting at Duel Academy, which suggests that they did know each other previously. Also, Johan's body structure and the way his hair is styled is similar to the female side of Yubel.  Finally, when Yubel returned to Earth, supposedly all but her left arm was destroyed on reentry - but was it? Yubel is shown to have many powers, including reality-warping, possession, and reconstitution through duel energy. What if Yubel's energy just scattered and part of it reconstituted as a separate entity? It would explain Johan's Expy status for Judai and why we don't know anything about him beyond his dueling achievements.

Fubuki Tenjoin is a flaming homosexual; Darkness is the embodiment of his attempt to suppress that and become a Ladies' Man, brought to life by his Shadow Charm.
First, he's obsessed with the pop idol shtick, so secretly-gay boy band jokes apply. Second, he's ridiculously showy even with his obsession. Third, despite his parading to the girls, he has yet to seduce any of them and has hidden from them when they started stampeding towards him - something that a true Ladies' Man would never do. He gives lousy dating tips to the heterosexual Manjyome, showing his lack of understanding of women.

So, why is Darkness his repressed sexual nature come to life? Simple: he takes all the above and strips away the facade of woman-wooing, making them manlier. Also, during his duel with Hell Kaiser, he makes two contradictory statements about his Super-Powered Evil Side: he says that it'll always be a part of him, but he later says that it's gone and will never come back. Note that the second statement is made under duress after Hell Kaiser questions his competence with his alter-ego's deck, wondering if it was him or it that was calling the shots. This could be Fubuki's acknowledgment that he's homosexual, but denial that he's ineffectual because of it. Plus, every other alter-ego in Yu-Gi-Oh! (except the ones that were another being entirely possessing the person's body) had been created from repressed emotions brought forth via a magical item (Marik and Yami Marik,, etc.). Fubuki was given one half of the Shadow Pendant, so...
 * Partially Jossed in Season 4: Fubuki wasn't the first or the only host of the Darkness entity, so it isn't the embodiment of his repressed homosexual angst. But that doesn't rule the gist of the theory out, especially since Darkness' last host was a bishounen pretty boy who just happened to be Fubuki's best friend.

Judai is destined to finish Yugi Mutou's last task: sealing up Zorc and the Shadow Realm/Duel Monsters Realm forever.
First, why else would Yugi give Judai a Light-Attribute version of Kuriboh, one of his favorite monsters (and the ka of the Nameless Pharaoh)?

Also, before and during Yugi's stint as the vessel for the Pharaoh, the only way for the Duel Monsters to become "real" was through Shadow Games. Now, several duelists have the ability to see Duel Monster spirits, and all that's needed to summon them is a specific holiday celebration or incantation that anyone can perform. It is also way too easy for Judai and the gang to use their Duel Monsters to reopen the portal back to the Duel Monsters dimensions in Season 3, hinting that the boundaries between the real world and the Duel Monsters dimensions are at their weakest. It's no coincidence that Yugi would give the light version of his Kuriboh to a kid that not only can see said Duel Monsters, but also has dueling prowess equal to or surpassing his own, especially once he gained his status as.

So why doesn't Yugi try and fix the problem himself? Because, despite popular belief, he didn't destroy Zorc during Memory World; he just resealed the fiend and is too busy with keeping that monstrosity at bay to do anything else. (Hence why he was gone from his Grandpa's for so long.) Yugi could sense the potential in Judai and gave him Winged Kuriboh as a "passing of the torch" to complete his mission and keep the two worlds separate. The final nail in the coffin shows up in Season 4; right after the gang's romp through the Duel Monster Universe triad, Kaiba's Hard Light duel disk imaging devices start malfunctioning, indicating that the veil between worlds is thin enough for the monsters to emerge without such assistance.


 * Another explanation to the weak barriers between the worlds is that Zorc is dead. However, because he was technically killed 3000 years ago thanks to some quasi-time-travel shenanigans involving the Millennium World altering history, "Darkness" as GX recognizes it was just a random albeit powerful shadow monster that fought its way into the power vacuum created when Zorc was ontologically erased from time and space. The barriers are super-weak because Zorc isn't presiding over the Shadow Realm with an iron fist anymore, allowing monster spirits to basically come and go as they please.
 * Shortly before getting zapped, Zorc gave the Pharaoh a Hannibal Lecture which may foreshadow Darkness's uprising in GX. Zorc says (in the Japanese version at least) something to the effect that all light eventually fades, no matter how bright it shines, but the darkness is eternal. Though Zorc was the alpha dog of the Shadow Realm at the time, he knew that something would take his place if the Pharaoh destroyed him. Darkness gives Judai a very similar speech after getting beaten, only remarking how Darkness himself is eternal!

Taniya is the Duel Monster Scar-Eyed White Tiger.
It's already been established in the Seven Star Assassins arc that the Shadow Charms can bring Duel Monsters to life in the real world (as the Eyepatch did for Don Zaloog). Once she was beaten, Taniya transformed into a white tiger looking similar to Scar-Eyed. Also, she pops back up in the second of the Duel Monsters dimensions in season 3; if she wasn't a Duel Monster, but a regular tiger, then how did she get there? Then there's her "pet" tiger that looks exactly like Amazoness Tiger and could be the monster come to life...

The Abandoned Dorm wasn't an alternate Obelisk Blue boy's dorm, but a specialized dorm for students who could see Duel Monsters spirits and had other duel-related special powers.
The dorm had only been abandoned for a year before Season 1. It's not impossible, given Kaiba's access to massive amount of funds, but it's unlikely that a brand-new boy's dorm would be constructed within that time. Plus, there's the relics of the ancient ancestry to Duel Monsters in the abandoned dorm (which no other dorm has, and likely no other dorm will ever have, given Kaiba's refusal to believe such nonsense) and its own ritualistic Duel Arena (again, something none of the other dorms have). Plus, if we're to believe that the dorm was abandoned because of an attempt to recreate the Millennium Items, having it be home to the school's more preternatural students makes sense; sacrificing such people would give more power to the Items. Fubuki was called there because of his connection to Fujiwara (who has his own Duel Spirit partner, the monster Honest) and the ritual Fujiwara performed to bring back Darkness.

The reporter who was interested in the Abandoned Dorm incident was paid off or killed by Kagemaru to keep the story secret.
He swore to the gang that he'd help them find out the truth behind the incident, and then vanished with no word on whether he got the story out. Considering how hard the school tried to keep the incident under wraps, it's likely he was silenced with either money or a bullet to the head to keep the truth from being leaked.

Duel Academia is an orphanage where the kids are kept happy by having them play a collectible card game all day.
First of all, Duel Academia is owned by Seto Kaiba, who is himself an orphan; in the original series, he did seem to have a soft spot for orphans, though he would never admit any such weakness. Second, the only parent we ever see is Hayato's father; given how he feels about his son, it's not impossible that he disowned Hayato after he failed his exams for the second time. Third, after Fubuki returns from the Shadow Realm, neither he nor Asuka make any visible effort to contact their parents about his return. You'd think that they'd want to know that their missing son had reappeared. (Granted, the school is engaged in a massive cover-up about the missing students, but how hard is it to send an email?).

Judai is the reincarnation of Yoh Asakura from Shaman King.
In Shaman King, when Yoh was reincarnated, his soul was split in two. One became Yoh, the other became Hao. In Monster World, when Judai, he goes by the name Hao. Evidently, Yoh's and Hao's souls were recombined some time after their deaths and returned to Earth as Yuki Judai, but remained in conflict; Yubel was able to force Hao to the surface.

The original Yu-Gi-Oh! is a Show Within a Show on Neon Genesis Evangelion, and GX is another Instrumentality-induced fantasy imagined by Shinji Ikari.
Shinji, the ultimate Unlucky Everydude Non-Action Guy in a painful, Deconstructed shonen universe imagines himself as a popular, talented, fearless, perfect, ultimate, too-good-for-words hero in a classic shonen series. He doesn't get the least bit nervous around Asuka, and Rei is an emotional, energetic, spunky young admirer of his. But, as Shinji rejected Instrumentality for the real world, the fantasy started to wear thin. The characters he imagined all started disappearing, and Judai's Hidden Depths were revealed as his own world and psyche started falling apart.
 * Would Johan be a re-imagining of Kaworu in this scenario, then?
 * Alternately, Neon Genesis Evangelion is the Show Within a Show, and Judai has been watching it way too much.

EVERYTHING in Season 4 is a hallucination by Judai after his fusion with Yubel, and/or the fusion/destruction of reality as he knows it.
Nothing so far in Season 4 makes sense; not Trueman, not Yusuke Fujihara/Honest, not the punk Psycho Style duelist who wants to crush the Cyber Legacy, none of it. Worse yet, the deeper we get into the season, the more confusing things get. They don't explain why the Duel Disks were acting up in the season's beginning, they barely explain Darkness' connection to the Abandoned Dorm (and the Dorm was destroyed before anything else could be divulged about the incident that happened there that Kagemaru was involved in), they don't bother to explain how Hell Kaiser Ryo survived his "death" last season and returned to Duel Academy, Honest's part in everything was never touched upon after he fused his soul with Judai... and Trueman has nebulous plans that seem to involve molesting disgruntled little boy duelists to negate the existence of all citizens in Domino City and Duel Academy. The only thing that can possibly explain this Mind Screw of a season is that Judai failed to cure Yubel's madness after they fused at the end of Season 3, became infected by it, and is slowly going irrevocably insane.

That, and/or his fusing with Yubel didn't prevent all the dimensions from fusing into one and becoming destroyed, as he hoped it would. His Heroic BSOD has deepened into pure psychosis from the aftermath and his knowing that, in the end, he couldn't save anything.
 * Or maybe when he fused with Yubel, it destroyed his mind. Season 4 was a desperate attempt my Yubel to make Jaden happy by putting him into a dreamland, but only just. Jaden coming back to Duel Academy, saving the world again, and dueling Yugi was all just part of that. Jaden's sorrow represented the damage done to his mind.

Kenzan lied about the origin of his dinosaur DNA.
Fossils are formed when organic material decomposes, and the remaining void is filled with minerals. To overly simplify things, a fossilized bone isn't a bone, it's a rock in the shape of a bone. Yet Kenzan claims that his broken leg was repaired using a dinosaur fossil. So what's with the Hellish Pupils?

Kenzan is a vat-grown hybrid clone. He and his ilk (dinosaur DNA is just the latest in a long line of human-animal hybrids) are grown as genetically engineered soldiers to be sold to the highest bidder in the event of a future war. Kenzan managed to escape the clone factory in his youth and successfully infiltrated human society. He now makes up crazy stories about the origin of his strange eyes and abilities to throw off suspicion. Despite all this, he still manages to be one of the happiest and most mentally balanced characters of the cast; this demonstrates just why his Tarot card is Strength.
 * Dinosaur DNA has been found in fossils. And with the Shadow Realm next-door, there's been MUCH weirder shit happening anyway.
 * If Kenzan is a vat-grown hybrid clone, maybe he was sold to the highest bidder. Kaiba is in charge of Duel Academy, right? And if Kenzan is good at dueling, he's worth every yen.
 * Or maybe he fused with a Duel Monster ?
 * Eustace Bagge got away with getting a fossil transplant, and turned into a kangaroo monster, so...

Misawa and Taniya did a lot more than "dueling all night."
Seriously -- what else are you going to do with someone bound to be your husband for only one night? The screams during the night, the PTSD-esque withdrawal the day after, the overwhelming desire for acceptance the next season and his ceasing to be a self-proclaimed Celibate Hero... something traumatic happened that night. Clearly, he lied when he told the others that they spent the night dueling. (Wouldn't you if you were him?) His pleasant demeanor around her in Season 3 only makes the implications worse.

And Misawa wasn't the only one who got spanked by a Duel Monster in the series...
Take a look at Judai's severe change in character post-Yubel soul fusion, then remind yourself that the main goal of Yubel for the third season was to make Judai its love slave and "convert" him to its form of sadomasochistic love. Then remember that Yubel admitted to orchestrating Judai's transformation into Supreme King Haou. And poor Asuka never suspected a thing...

The entire cast (minus Judai) is slowly being replaced or bumped off.
First it was Misawa staying behind to hang out with Taniya; then it's Asuka choosing to study abroad after she can't get into Judai's pants; then Sho takes over the role of Kaiser from his nearly-dead brother; and now Manjyome is screwing up Edo's career as a professional duelist and taking his place. As the fourth season is the graduating year for all the characters, this might be justified as an example of how old school friends go on with their separate lives after school ends. But this sudden push to get all of the old characters out of the picture is too blatant to be coincidence.

Jun Manjyome's mother died in childbirth.
Jun's older brothers put pressure on him to uphold the family name - not his parents, who should be more concerned about stuff like that. When he runs away and isn't seen for three months, his brothers are waiting for him when he returns to the Academy. No parents. In the beginning, it's only his brothers he wants to please, not his parents. It's his brothers' help he doesn't want to rely on to become a pro, not his parents, who would logically be the ones with the money and connections in high places - if they were alive.

Conclusion: they're not around, out of the picture - dead. After the Manjyome brothers become estranged, Jun still has an unlimited supply of money to spend on things like building his own private dormitory with a jacuzzi; clearly, he's living off a trust-fund. And why else would his older brothers despise him so much, even when he was a top-ranker in Obelisk Blue? They blame him for their mother's death (or so every other Fanfic about their childhood says).
 * The thing is, Jun's brothers don't hate him. They won't accept anything short of the best from him, and the fact that he can't be number one drives them up the wall, but it's a bit of a stretch to say that they despise him.

Season 4 was purposely cut short to cover problems on the set.
Many coincidences seem to point to this: first, unlike the other three seasons (which went from February to October), the fourth season is shutting down by March/April, half that time. Also, its replacement, Yu-Gi-Oh The 5D's, and its cards are being pushed awfully hard, with the first set of the new show coming about the same time the anime debuts - which means the GX group of card sets (from The Lost Millennium to Light of Destruction) is a full two or three sets shorter than the original anime's group (from Legend of Blue-Eyes White Dragon to Flaming Eternity); the missing three sets would've filled the gap had GX continued as scheduled. There's also the nonsense of the fourth season's premise: nothing about antagonists Fujiwara's or Trueman's motives for their actions (or their actions themselves) makes sense; the suddenness of minor villain Darkness rising up to be a Big Bad is equally puzzling; and many loose ends from previous seasons (like what really happened in the Abandoned Dorm incident, of which we know nothing except that Darkness had very little to do with it) remain unresolved. It's very likely that, had the show went on, Darkness would not have been the final Big Bad; he is only because the writers had to rush to get the show some closure after it was cut in half. Finally, there have been rumblings that the voice actor for Yuki Judai was demanding more money for his performance in the fourth season, money that for whatever reason the producers refused to shell out. All this seems to indicate that something happened behind the scenes to make the producers want to cancel GX for good and use the new series to defuse the backlash.
 * See the Just Bugs Me page for a full explanation of the evil plot. It's also been rumored that Judai's voice actor was fired, and so they decided to promote the Disc One Final Boss to Big Bad and rush 5D's rather than replace him.
 * It flies in the face of what was established in the show itself. Darkness wasn't involved in the Abandoned Dorm incident, nor was Fujiwara or Trueman. The real reason behind it (that is, the reason Kagemaru set it all up) is still unresolved. Darkness should've been a Fake Boss; something else was to be the Big Bad, something that probably would've explained the reasons behind the Abandoned Dorm, Darkness, etc. As a result of the show being cut short, the writers were forced to condense the storyline to bring the series to a close - and did it badly, resulting in a nonsensical and confusing Mind Screw of a season.
 * Judai's VA started demanding a pay raise when the season was halfway done. Since the producers didn't want to change voice actors for their most prominent character, they cut the season short and rushed the storyline to spite the bastard.
 * This explanation is kind of hampered by the fact that KENN is still voicing Judai to this day. So try again, kid.
 * But that's only for the Massive Multiplayer Crossover anniversary movie; paying an actor to come back for a single movie is nowhere near the scale of paying a higher salary for that same actor to replay his role for dozens of episodes. So, basically, the theory is still valid; they refused to give KENN a bigger pay raise for the fourth season (which would've given him at least two dozen episodes worth of pay raises), but were able to work with him on a single movie (which would've been one lump sum they could manage).

Everything from Season 4 happened only in Judai's head
Yubel is a Magnificent Bastard of the highest order. Judai, upon fusing with Yubel (her real goal, don't forget), became trapped inside his own mind, living out an elaborate fantasy while Yubel took control of his body and quietly subjugated him. His sudden appearance in a desert marked the completion of this process, and "Banner" is a shade of Yubel intended to keep Judai under control.

Alternatively, everything from the first appearance of Rainbow Dragon onwards didn't happen
...and both Judai and Johan are trapped in the Yubel card, along with the monster herself. As above, everything from there is a fantasy cooked up by Yubel to suppress Judai.

The whole of Judai's duel against Yugi was a hallucination
How else do you explain Judai going back in time, time stopping for his and Yugi's duel, and the duel ending with no conclusion, only for Judai to randomly be in a desert with Pharaoh/Daitoukouji randomly in his bag with a letter from home?

Kaiba founded Duel Academia to make up for how uselessly antiheroic he was during the original Yu-Gi-Oh.
We know Duel Academia was founded by Kaiba. It is later revealed that its purpose is to attract the superpowerful cosmic whosawhatsits and train kids to beat them. Kaiba was rather... against the idea of the paranormal back in the day, and thus was more often than not an obstacle to getting the world saved. Between the two series, he realized how much danger he put the world in due to his pride and made a place to do the world-saving in the foreseeable future to make up for it.

Kaiba didn't make Duel Academy to repent, but to continue his rivalry with Yugi; it's a giant attempt at one-upping Yugi's heroism via saving the world through his students.
Proof of this is shown in the way the dorms are listed. Obelisk Blue (Obelisk being Kaiba's personal God Card) is on top, and Slifer Red (Slifer being the first God Card Yugi got a hold of) is only for "slackers".
 * Ironically, Yugi is still beating him; the student saving the world has only been able to do so, and has only made it this long, due to Yugi playing the mysterious mentor in episode one.

Yubel was male in his life as a human, but was castrated upon being turned into his current form.
He was young enough before the surgery to be androgynous, so no one knows for sure what his real gender was. Since the purpose of his transformation was to protect past-life Juudai until he reached adulthood, this would probably have been done as a measure to prevent him from becoming distracted from his duty. Also, Yubel has two voices, the voice it had as a human and a deep male voice which is never explained. If this is true, the male voice would be the voice Yubel would have had as an adult if he had stayed human, possibly indicating that he feels some regret for being turned into...whatever that thing is.
 * Except for the fact that a boy's voice deepens during puberty because of increased testosterone levels, which are produced by the testicles.
 * Or maybe Yubel was a Hermaphrodite with the physical appearance of a girl prior to losing humanity...

Season 4 didn't happen because Judai's fusion with Yubel lead directly and immediately into the events surrounding Zero Reverse.
The garbage surrounding the ancient history of the Jibakushin and the Nazca Lines are all blatant lies, and the Jibakushin have only existed for as long as Yubel and Judai have been fused. Furthermore, Rudger's destruction of Old Momentum which caused the Zero Reverse was a desperation bid to prevent Instrumentality - had Yubel and Judai not become fused, Zero Reverse would have turned into a black hole that ended all life in this and every other reality, and without Zero Reverse happening, everyone would have become tang. The two events canceled each other out, containing the catastrophe to a manageable area and leading directly into the Oddly-Named Sequel 2: Electric Boogaloo, 5Ds.
 * Alternatively, Zero Reverse could have happened as a direct result of Trueman and Darkness' actions. Namely, that the entire population of the planet just suddenly up and vanishing while some people are, say, in the middle of conducting open heart surgery, would be rather catastrophic.

The show is the result of a dimensional warping caused by Anubis.
Remember Yu-Gi-Oh the abridged movie? How Anubis showed the characters the grim future? Anubis actually caused this horrible fate by warping reality.

The plot of GX will be resolved in 5Ds.
Similarly to how Judai went back to duel Yugi, Yusei will go back to duel Judai, but Yusei will stay and fix some things.

The Entire Series was a Writer Revolt by the original creators of the first manga.
They were sick of how their Dark Anime about an Evil avenger had mutated into a Merchandise-Driven commercial for a card game that was only originally intended to be featured in a single story arc, so they made another series that was pure horror and one constant Take That at the tropes the original anime series was built on.
 * That...makes so much sense! Especially if you consider that the first series pre-Duelist Kingdom Arc had more games and challenges featured than just card games...
 * Makes no sense. Takahashi was more involved with the original manga (card games and all) then he was with the second series. I don't think he did much besides designing characters and monsters.

Johan and his deck are a veiled shout-out to Bifröst.
Johan uses a rainbow-themed deck, is Scandinavian and wants to connect humans and spirits. Bifröst is a rainbow bridge in Norse mythology that connects Asgard, the realm of the gods, and Midgard, the realm of the humans. Sound similar? There's also Johan's speech in 130: "Rainbow Dragon, fly! Become everyone's bridge..."

In the ten years between Yu-Gi-Oh and Yu-Gi-Oh GX, Kaiba took over the world.
It would explain why trading cards are used in politics and scientists. After the main series, Kaiba realised that the Shadow Games were real, and he could use his link to the past to make his holograms real. The Kaiba you see is actually Mokuba, who is in disguise so Seto can rule the world in secret.
 * Then who's Mokuba?
 * Shut up, Mokuba.
 * That WOULD explain why Kaiba doesn't appear to have aged and Yugi has.

The series is an AU, having diverged since Season 3
In this timeline, Gozaburo managed to digitize the world. However he failed to become a cyber-ruler as he lost the battle with Kaiba, who used his techno-wizadry to remove Gozaburo. He decided to reprogram the virtual world so it fit his desire-a world run by a card game.

As no-one knew who Noah is and he was never mentioned by anyone in GX, it's safe to assume no-one noticed becoming digitized (much like the Matrix). Yami Marik is still on the station, having starved to death. Joey created a copy of Mai's mind to deal with the loss. Yugi has spent his time adjusting to what happened. Monster spirits are holograms which have gained sentience,and the Light of Ruin is the remains of Gozaburo.

Fubuki was being influenced by Darkness to release the Shadow Beasts
When Manjoume came to Fubuki for advice in wooing Asuka, Fubuki himself was at his weakest; off guard, relaxed, and unnoticing of what his actions could really cause. Under influence of Darkness, who still had plans, Fubuki "came up" with the idea of Manjoume stealing and using the Gate Keys to battle Asuka for her hand. This in turn was the sole cause of the Shadow Beasts gaining the energy needed to reawaken, almost bringing about The End of the World as We Know It in the process.

4Kids haven't dubbed season 4 of GX yet because they're trying to fix it
Because their voice actor isn't asking for more pay, they're trying to extend and clear up the season. Of course, this is a lot more work than they usually do, but if this WMG is right, they might give us a non Mind Screw, fleshed out season 4 with a new Big Bad after they finish dubbing 5D's. I might be wrong, but hey, 4Kids don't have to screw everything up.
 * Jossed by the death of 4Kids.

Yu-gi-ho GX is in the same universe as Persona4
As in persona, everybody uses cards, except it's so far in the future they have developed entire decks of them: each monster is a persona (which is why they can be seen as spirits), traps work as items, etc. Thus the Yellow Eyed Supreme King is actually Judai's shadow, contrasting and deconstructing his personality as the talented yet normal ace who only plays for fun, and it ends up being accepted as part of Judai's. Thus, the darkness is the master of fog which is why no one really dies and the world is so far in the future that shadows now have the power to shape shift themselves into humans.

The vision of the future that Darkness shows Judai is the Bad Future of Zone, Aporia, etc from 5d's
Don't deny the similarity.

Jaden's deck has an ultimate Hero
But it isn't an Elemental Hero, no, it's The Goddamn Batman! He can summon it by fusing every non-fusion E-Hero in the Fusion Gate, but Fusions can be used to count as all the monsters fused to summon it, and if he used a substitute fusion monster, it wouldn't count. Due to this difficulty, Jaden has never summoned The Goddamn Batman.
 * Actually, it's likelier that the sum product of all Jaden's Elemental Heroes is Superman. Besides, Bubbleman is already a parody of Batman.