Ansem Retort/WMG

Axel will knock Aerith up.
There is absolutely no reason to think this other than the number of hilarious situations this could involve, starting with everyone else's reactions. Plus it looks like Axel actually kind of does love Aerith, so he might turn into a twisted version of a Papa Wolf...not to mention what the kid might be...
 * Yeah, but the really ironic thing would be for Aerith to knock Axel up instead.
 * The other ironic thing would be if their kid was the exact opposite of them: whiny, weak, and emo. Hold that thought.
 * Except Riku already fills that niche.
 * You haven't looked at the next WMG, have you?
 * For record's sake, THIS IS AN APRIL FOOL'S JOKE.
 * apparently confirmed. Still too soon to be completely sure, though.
 * Confirmed, and then promptly aborted. We should have seen that one coming.

In the Alternate History, Axel is actually peaceful.
Check this comic. Notice anything? At least half the people in the background were people murdered by Axel in the proper timeline. Their being alive now could mean that Xemnas's manipulations have made Axel non-homicidal, almost pacifistic...just as planned.
 * Jossed by Word of God
 * And, you know, the fact alternate!Axel dropped Riku into a volcano and then nuked it.
 * Well sure, after his Original Memories were reawakened by the Power of Andrew Jackson.

Axel shot JFK

 * While we're at it, have him kidnap Harold Holt. Just to prove he can fuck with other nations' heads of state too.
 * Next target: the Princes in the Tower?

When the series ends, Axel will burn another orphanage down.
Come on, who can resist the Book Ends?

Riku is Axel and Aerith's kid from the future.
Why not? Time travel's already in play. And the irony of a murderer and a psychobitch having an emo kid for a son would be hilarious. Plus, given that they'd be Abusive Parents before they knew and probably worse after they find out, either Riku would succeed in killing himself, or takes a level in badass, and (for the hell of bringing his name up) becomes Sephiroth.
 * Not actually 100% sure they'd be abusive as parents (Axel has never, ever actually hit Aerith - he actually got kind of pissed when she pretended he did - and that might extend to his kid, and Aerith is snarky, snappish, and  is a Magnificent Bitch, but she doesn't seem to do hands-on violence.) Plus, don't you think he'd say "HOLY SHIT I'M WATCHING MY PARENTS HOOK UP" or something?
 * Yes, he'd probably say that, if he wasn't both severely brain damaged by all the blunt-force head trauma and vulnerable to Namine's memory-based whimsey. Even if he is their son, he probably doesn't remember anymore, and won't remember until it is comedically/dramatically most appropriate, at which point the memory in junction with seeing them hook up will make him want to kill himself. Er, moreso.
 * I'd like to also suggest that this is why Riku's the only one that realizes that  Only time travellers are immune to effects like that.

Riku is playing The Reaper's Game!
Red XII has fullfilled his promise to eat Riku's parents. That means that Riku no longer exists eg. dead. This explains the sudden use of TWEWY backgrounds, and the appearence of Axel's murder victims in the background. As I stated above Xion will get involved, fighting for existence with Riku as her partner. Oh.. a Kairi will show up as a reaper.
 * Jossed, Riku is immune to time changes, because he is.

Riku can remember the "real" past because he isn´t human anymore.
Because of the maaaaaaaaaaany surgeries Zexion performed on him, his body (including his brain) consists to 99% of straws, hotpockets and other makeshift organs. Therefore he is some kind of "Miscellaneous-Golem" and not affected by the changes in world history, because his conscience is different from other human´s.
 * Well. He's certainly not human,  So semi-confirmed?

If there is a Gender Flip Alternate Universe, then Larxene is the counterpart of Doctor Rockso.
Well, let's look. Both are drug addicts, and are willing to sell out and betray supposed friends for their next fix. Both of them are naturally blond. (The discrepancy in skin tone's harder to explain but no WMG is perfect.) Both have definitely been around things that aren't normal (Red XIII vs. Dethklok, Xemnas vs. Selatcia.) And whoring himself out on a reality show that embraces, nay encourages drug use isn't out of character for Rockso. Presumably, though, if they are the same person, different gender, then Larxene is also a future version of Rockso, due to going from cocaine to...everything, and from the world already gone to hell. In other words, Ansem Retort takes place in a post-Metalocalypse alternate universe.

Alternately, they take place in the same universe and Larxene is one of Skwisgaar's many children.
Well, there is the blond hair...plus, if the 'Skwisgaar is the son of a god' WMG is true, it's quite possible that that is where Larxene's lightning powers come from, especially if Skwisgaar's father turns out to be Thor.

Kairi won't come back to life. She'll become a werepire.
Or a Reaper, It depends on whether or not they use The World Ends With You plot points rather than just the characters. The both are technically dead so it's a case of Exact Words.
 * Either way she won't coming back into comic by the Word of God.

Kairi will come back to life/become a ghost/zombie/what have you...
and kill Axel for killing her.
 * Word of God says she's not coming back.

If Axel and Darth Maul fused, they'd turn into Theodore Roosevelt.
Cause he's the only thing more badass than Andrew Jackson. Also, he totally used the Force. I don't care what you say.
 * You're missing the point. They became Andrew Jackson because Axel was a murderer and Zexion was a politician, which Andrew Jackson was both of. If Axel fused with Maul, he'd just become a Murderer who is also a Sith Lord and a Jew.
 * Sooo, Adolf Hitler? He was Jewish.

In the fanfic Geishas of Winter, the orphans that Crocodile was raising money for were the orphans who were displaced when Axel burned down the orphanage.

 * Even though the orphans and the orphanage aren't stated, it is a strong possibility that Crocodile was helping out the orphans displaced by the fire Axel set.

Zexion will eventually become president.
President Evil, naturally.
 * Technically semi-confirmed, as Zexion and Axel have the power to fuse into ANDREW JACKSON MOTHERFUCKER!
 * He is Governor Evil. Close enough.

Everything is a big Xanatos Gambit...by Goofy.
Of all the important characters in KH, there has yet to be a use for Goofy's sprite at all. And let's face it, he'd be the last person you'd expect to be behind everything.

Xion will get involved in this somehow.
With all the reality alterations its possible that she, not, Kairi was sent to the reality TV show mansion. Because she can fight she survived the first season. However her sprite will just be a Kairi Palette Swap. Riku will develop a crush on her due to the fact that her life has been Deus Angst Machina but will break up when she finds out that she's a Male-To-Female transsexual.
 * And what's worse, she's still a Yaoi Fangirl. She's spent most of the time here trying to get Axel/Zexion and Darth Maul/Marluxia to make out. Or something.

We haven't seen the last of Yuna and (girl)Rikku.
Red XIII joined the main cast, the others were slaughtered by Axel, but all we know of Yuna and Rikku's fate is they went to dig to the center of the Earth at the Vatican on Darth Maul's suggestion. I wouldn't be surprised to see them pop up again riding an aeon or something, stopping whatever enemy it was this season, then promptly getting eaten by the aeon, who will become the next villain.

Marluxia is either going to die or turn into a monster.
Axel, Marluxa, Riku, and Zexion went back in time. Who came back was Emo Mode Riku, Andrew Jackson, Jesus, and an unidentified monster (Heartless). We know about Axel and Zex being able to fuse into Andrew Jackson, and they just recently picked up Jesus to join them, so the only things unexplained is what happened to Marluxia and who the new guys is. One of these things happened:
 * Marluxia died and the monster is someone they picked up to be the new token gay.
 * Marluxia went One Winged Angel and turned into the monster.
 * It looks like Jesus is gonna transform Marluxia into the dragon.