Assassin's Creed: Revelations/WMG

When you play as Altair in Revelations, you will be able to swim.
Because the official explanation for Altair's sudden swimming deaths is that it's an Animus glitch. Since Desmond is in a different Animus and Ezio is not in an Animus at all, that glitch will not exist.
 * ... Alternatively, you still won't be able to swim because Altair really was hydrophobic.
 * Sidestepped,.

Ezio and Altair have superpowers beyond eagle vision
courtesy of being descended from those who came before. There's no other way Altair could live to 92 in the middle ages, not to mention Ezio being just as physically capable at 52 as at 19. They have enhanced strength, endurance, and longevity.

We will see Ezio die onscreen at the end of Revelations
What better why to end the final chapter of his story? The genetic memory could be hand waved by Ezio being killed in the presence of the mother of his child, moments after they've made love, or it could even be witnessed by Ezio's infant son or daughter.
 * Doesn't even have to be directly related to Ezio. If anyone who was there to witness Ezio's death eventually winds up on Desmond's ancestry, this could be justified.
 * Jossed: The animated short Assassin's Creed: Embers will have Ezio quite old and gray, have a family, and still remain just badass enough.

We will see Altair die onscreen at the end of his final seal memory
He isn't even protected by the whole Genetic Memory angle now, and if The Secret Crusade is anything to go by.

Altair is still alive in 1512 and Ezio will encounter him
He managed to use the Apple to give himself a much longer life, as implied by the final codex page in AC2. What he's up to in Constantinople is anyone's guess.

Following on from the above WMG...
Altair is the superweapon hidden under Masyaf.
 * As an extension: Altair is a rotten corpse when Ezio finds him, because the Apple made Altair mad and think he could survive being locked in that room for several centuries.
 * After four centuries? Make that a skeleton or a mummy at best.
 * Actually

Ezio is experiencing the Bleeding effect
And that's how he's seeing the shadow of Altair. Those seals he's collecting? Early forms of an Animus.
 * Technology from Those Who Came Before that formed the basis for the Animus.
 * Jossed (maybe?) as the writer of Revelations Darby McDevitt in an interview that Altair and Ezio are from different sides of Desmond's family tree, so Ezio wouldn't have Altair's Genetic Memory.

At the very end, Altair, Ezio, and Desmond will interact directly.
Somehow the Apple will bring the three together to simultaneously assassinate someone in one of the three time periods. Then they will chat and wonder WTF is going on.
 * Kind of Jossed and Confirmed. There is one critical moment in the game where the fates of all three characters converge.

Desmond will have a temporary personality takeover.
Due to the ever worsening Bleeding Effect, Desmond will briefly think he is Ezio. Conversely, Ezio will suffer the same thing, but with Altair. Or maybe both.
 * Jossed, though Desmond does have to share his Animus mindspace with.

Desmond will have a PERMANENT personality takeover.
That is, something glitchy will happen within the Animus, and Desmond's shattered mind will be completely overwritten by Ezio's memories, and Desmond will wake up, seemingly AS Ezio, in 2012.
 * Jossed. The entire plot of the game was for Desmond to piece together his original personality.

Ezio will convert to Islam in Constantinople
Because the Ubisoft team has already stated that the Turks by and large are more assassin friendly than the Byzantines who are waging an ongoing conflict against them, and have openly allied themselves with the Templars. Not to mention that the Roman brotherhood has been helping the Turks for years at this point. Could be done as a show of good faith (pardon the pun) to the assassins there, as well as established Ottoman society. And also because it'd be good PR to have a Muslim protagonist in a video game FOR ONCE.
 * Really not likely to happen. Ezio's a devout atheist.
 * Ezio could convert to Islam out of convenience, just to get by in the Middle-East more easily, but it's not very likely, since converts tend to attract unwanted attention from both sides of the fence.
 * Also, aren't you forgetting that most of the Assassins from the original game would have been Muslim or at least lived in a way that was very heavily influenced by Islam?
 * Not Muslim. Assassins are atheists - religion isn't quite compatible with the "nothing is true" mantra. They oppose both Muslim and Christian armies in the Holy land.
 * Some could still be religious. In Buddhism, there is no God and no permeance fo the soul, but Buddhism allows for adherents to follow other religious tradition if it helps them achieve their end goal of Nirvana, and some Buddhists do just that. Similarly, some Assassins may be religious because it helps them keep going or because they feel that acting as Assassins is the best way to adhere to their faith (ie, a Christian may become an Assassin because they feel that saving humankind from the Templar's plans is one way of doing God's will or that their salvation is necessary sacrifice for the good of many).
 * If you listen to Ezio's explanation of the Creed, "nothing is true" refers to the fact that the foundations of society (like religion), are fragile and that humans must take care of their own problems. Basically, the ideal Assassin would not let anything as unreliable as religion guide their actions.
 * As a note, Ezio has met Assassins who are Christian (see at least one unconventional nun in the Second Game). Altair is an atheist as of his writings but Ezio, himself, never expresses any religious preference whatsoever and can build a church in his home town.

WMGs on the moment that connects Altair, Ezio and Desmond...

 * Losing a woman they loved. Ezio lost Cristina, Altair lost Adha and possibly outlived Maria and
 * Would explain Juno's actions.
 * Losing their father before they have reached manhood, maybe?
 * The game shows that the moment is when.

By waking himself up from his animus coma, Desmond will learn to control the bleeding effect
It seems like the best way to give him the ability (which it's always been likely he would obtain, given Shaun's Foreshadowing in Assassin's Creed II), short of zapping him with The Apple.

Claudia will be a skilled enough assassin on par with Ezio.

 * It's one thing that she was made one in Brotherhood, but I'm sure we'll see her parkour her way across Turkey as well as some killing.
 * Unfortunately, she never makes an appearance in the game so we may never know.
 * According to the Encyclopedia Claudia stepped down as the Mistress of the Rosa In Fiore in 1504 and took on a non-combat advisory role to Ezio and the rest of the Assassins.

The 'One Who Came Before' known as Jupiter will have a hologram appearance
In the ACII ending three 'gods' are mentioned; Minerva, Juno and Jupiter. Minerva and Juno have each appeared in a game so far, and the three of them together form the Capitoline Triad of Roman gods, so it would fill out the symmetry nicely.
 * Seems likely. Ezio is collecting First Civilization artefacts, and a member of the Triad appearing in each of the games in Ezio's trilogy has even more symmetry.
 * As Ezio and Desmond has met one "god" each, that leaves Altaïr to meet Jupiter, possibly through the Apple.

Desmond will wake up in an Abstergo animus
When Desmond gets out of the Animus at the end, the mind screw will be he's being held by Abstergo. Of course Abstergo don't realize that he's now as much as an unstoppable murder machine as Ezio and queue Assassins Creed 3 set in the present/future with Desmond as the main character.
 * Jossed.

Desmond, Ezio, and Altair will be brought together by "One Who Came Before" or a Piece of Eden.
Given the internal logic of Those Who Came Before and their artifacts, e.g. Minerva noticing Desmond behind the Animus' camera and the Apple showing only the Pieces of Eden that exist in the present day, It seems logical that either an artifact or One Who Came Before would pull all three of them "out of time" so that they can interact. In this vein, the moment in history that connects all of them would be their encounter with that entity or their activation of the artifact which allows them to meet.
 * Confirmed, sorta:

The moment that connects Altair, Ezio, and Desmond is a thing: the Apple.
As far as we know, the last three people to interact with the Apple are the protagonists. Maybe that wouldn't have meant anything had it just been Altair, Ezio, and someone else, but Desmond is the link between the two, and his presence makes that significant.
 * But Ezio put it under that Church in Rome before he went off to Masyaf. The model for Ezio when Desmond sees his ghost placing it on that pedestal is that same as in the normal game. Therefore, unless another Apple suddenly materializes (Time-cloning perhaps?), Ezio won't have it with him.
 * Jossed?.

Subject 16's mind is also stuck in the black box
He might serve as Mission Control during the Desmond segments.
 * Not just Subject 16, but perhaps Subjects 1-15 as well.
 * Jossed with Subject 4 at least (if you've read The Fall).
 * Jossed with Subject 4 at least (if you've read The Fall).

Altair and Ezio are alive because the Apple of Eden bestows immortality, though doesn't affect again.
Tying further back into the above WMGs, Altair and Ezio are alive and still secretly running the Assassins. They either work above, with, or actually are William. This is why Cesare kept screaming about how he could not die, because he knew that is what the Apple does. Which means that Rodrigo and Al Mualim are still alive too.
 * Not necessarily. Perhaps the immortality bestowed by the Apple is the kind of the First Civilization: They're immortal to age, but can still be killed by disease or murder.
 * Jossed:

All of Desmond's experiences thus far have taken place in the Animus.
Everything: his imprisonment at Abstergo, the escape with Lucy, working in the Animus... they're all memories, being relived by Desmond or Desmond's descendant. None of it is really happening.
 * This would explain the video-game like controls and Animus-style prompts outside of the Animus.
 * Or the Desmond sequences in the first three games are memories, but they're being relived by Desmond sometime between Brotherhood and Revelations, during his Animus coma.

Duccio de Luca will show up in Constantinople, pissed off and ready for round three.
In both Assassin's Creed II and Brotherhood, Ezio has a fist fight with Duccio (an ex of Claudia's), though admittedly in Brotherhood he shows up in DLC only. Revelations will have Duccio pop up at some point in Constantinople (Brotherhood notes he did become a trader, after all, albeit a very bad one), and will want to try and even the score with Ezio, so instead of fighting one-on-one or with a group of thugs, Duccio will instead have armed mercenaries or paid-off guards to help him defeat Ezio. He'll defeat them all and leave Duccio lying unconscious and bloody on the ground one last time. "Duccio: Le diavolo in persona! (The Devil Himself!)
 * Confirmed.
 * Chances are he's probably going to harass Sofia, cue Ezio's fist to the face.
 * Sadly Jossed, as while Ezio jokingly sings about their rivalry, Duccio's only harassing Sofia. When Ezio interrupts them though, cue this gem of an exchange:

Ezio: Duccio. A pleasure.

Duccio: Run, buona donna! Run for your life! [runs]"


 * The achievement/trophy is called "Bully", where you have to find and beat up Duccio. If anything, the title implies that Duccio's done nothing wrong this time and Ezio just wants to fuck him up some more, just for the fun of it.
 * In this case, Ezio just finds Duccio wandering around drunk in the city after scaring the hell out of him, so basically Confirmed.

There will be an achievement/trophy tied to giving out money with your Assassin Robes dyed red.
Because you are playing a rather jolly old man with an impressive beard and a fur robe. In Turkey. Also, why the hell not?
 * Achievement list is up, and sadly, it's Jossed.

Subject 16 will show up in the Black Room
There are already short clips on IGN's youtube page where a strange man is telling Desmond about a "Sync Nexus" and how to escape the animus.
 * http://youtu.be/pTXvFqHvMBg?t=56s
 * If the above theory, that Desmond is being held by the Templars, is true he could even be a Templar agent crawling around inside Desmond's brain. That is some creepiness.
 * Confirmed to be Subject 16, more fully formed than ever.

We will meet (or at least find out about) the modern-day Templar Grandmaster, and he will be Zasalamel.
Zasalamel's ending in IV shows him to be alive in the modern day, with an interest in guiding mankind's development throughout time. It also shows him to be quite wealthy and powerful. And since Ezio does NOT travel from another dimension to be in Soul Calibur V (like previous guest fighters did), but is in fact a native of that world (with Desmond watching through the Animus, if my information is correct) then Zasalamel became a Templar at some point, or always was one, and is now Grandmaster of the order and the corporation he owns that his ending in IV hinted at is in fact Abstergo. Also, how awesome would this be?
 * And now Ezio is in Soul Calibur V. If Zasalamel shows up as well, it could be the start of an eternal rivalry between him and the Assassins.
 * OR it could be that Zasalamel is actually an ally of or an Assassin himself, as he didn't seem to have the Knight Templar sort of mindset in his ending of 4.

16 didn't WANT to live/be set free
It would explain why he seems to know everything, he's hacked into the Animus to access a ton of memories (err) and speaking through the Animus was his only hope of making contact with an Assassin. That, or he wentcrazy with power.
 * His body's "worm food now," making any such pretensions futile, and he knows it -- so in the end.

16 is the main villain
Tying into the above WMG, but just think of the power he now has. He's probably gonna upload himself to the satellite or something...
 * Jossed, sadly:

Ezio is the ancestor to The Most Interesting Man in the World.
"Sophia: Who are you, Messere? Ezio: Only the most interesting man in your life."

Claudia is the acting Mentor while Ezio's on his trip.
And maybe she took over full time after
 * Isn't Machiavelli more high ranking?
 * Confirmed with the novel of the game that Ezio leaves Claudia in charge of the Assassins in Italy during his journey, but bequeaths the role of Mentor to Ludovico Ariosto when he retires.

Ezio multiple times in his life.
It's just that only the time  had any effect.

The object Ezio gave Shao Jun
...Was the blade mechanism for the Hidden Blade.

Embers is a Poorly-Disguised Pilot for Assassin's Creed III
In that it features Shao Jun, a young Assassin with a very similar wardrobe to Altair, Ezio and Desmond (down to the pointed "eagle's" hood, something none of the other named Assassins in pretty much any game possess), and a mission that seems awfully similar to the plot of an Assassin's Creed game (taking down the corrupt emperor and the Templars behind him). She's young, but has a good reason to be leading the Assassins in China (the fact they were driven out by Jiajing), allowing the developers to keep the "Brotherhood" mechanic in place. Add to this that a few scenes in Embers imply she has free-running skills (she got to the roof of Ezio's villa without much trouble) and maybe even Eagle Vision (there's a pretty superfluous scene of her staring at something in Florence) and maybe we're looking at our next Assassin.

Getting back to the point of the WMG, maybe sometime after Ubisoft had decided on her for AC3, they decided to include her in Embers, explaining why it's half about her journey and half about Ezio's final days, rather than entirely about him.


 * This idea actually has considerable potential considering the political situation at the time. Considering that the Portuguese were establishing their empire around the Indian ocean at this time, this gives an opportunity to include vastly different cities in the game. Let's say that it starts shortly after Embers with Shao Jun arriving in Lisboa in order to catch a ship back to China. You could fight Templars in that city before you leave, then maybe a stopover in Goa before reaching Shangchuan Island and nearby Guangzhou and so on.
 * Wouldn't this require that Shao Jun is somehow related to Desmond? I guess it's possible to handwave her as being a great-great-(so on)-granddaughter of Darim or Sef, but that would be a heavy stretch.
 * Would not a relation in the other direction (that is, that Shao Jun is an ancestor of Desmond, rather than a relative of Ezio or Altair) be more likely, given the mechanics of the Animus? They do have quite a number of centuries to work in for merging the lines...
 * Not to mention that shortly before she leaves, Ezio gives Shao Jun a box and instructs her to only open it if she "loses her way". We never do find out what's in that box...
 * Plus, Shao Jun has a hidden blade IN HER BOOT. Imagine the amount of crazy new kill animations the devs can make on that alone!
 * Also, with one on each wrist, she'd have three hidden blades. In Assassin's Creed: 3...
 * Unfortunately Jossed. Ubisoft has confirmed that AC3 will take place during the American Revolution and that the protagonist will be a Native American.

The AI of 16 is a pretty incomplete version of his personality.

 * Without any memories other than the ones 16 uploaded while he was alive, explaining why Desmond can't just outright ask him about Eve or anything else.
 * Actually it's not incomplete. In this case, for the first time, we see a complete version of Subject 16, the version of him WITHOUT any ancestral memories to interfere.

There's a traitor high up in the Assassin Order
Reaching level 18 in the Multiplayer unlocks a dossier about the Animus. The last picture attached to the entry is of the Assassin-made Animus 2.0, complete with labels to identify key components. Unless Rebecca was sloppy with securing her notes when they evacuated the safehouse at the end of Assassin's Creed 2, the only way Abstergo could have that info would be if someone in the Assassin Order with access to info on the Animus 2.0 was a Templar spy.
 * If there was a traitor it was probably Lucy, programmed by Abstergo as a sleeper agent. Would explain why they try to subdue Desmond at the end of II with nothing but batons.

16 transferred himself to Desmond's mind after the Black Room

 * That long hug? Yeah, it was 16 implanting himself in Desmond's head. The man was desperate and actually asked if Desmond would let him. And hell,, so why would he ask again? He just went there and did it, and will return on AC 3.
 * Additionally, Ubisoft has confirmed that atleast four characters' voice actors will be returning. Said characters are Desmond, Shaun, Rebecca, and... Clay Kaczmarek? Now who could that be? Of course: Subject Sixteen.

Desmond will die in some seating implement
Let's look at the track record of his ancestors so far. Altair died in a chair and Ezio died on a bench. I would wager decent money Chairs, benches, and other sitting implements are actually all Templar agents.
 * Desmond could die in an Animus...