Ok, now, I imagine that NO ONE is probably going to read this, but, I'm pretty sure I know that Altair is going to be in the next game/games, and this is how they're going to be able to integrate him into the system, which is actually a pretty ingenius way.
If you read the email from Lucy to Vidic on his computer after you beat the game you will see that it says something about how prolonged exposure to the Animus caused a "Blood Effect", which basically was that the subject was unable to tell his world apart from his ancestors, or something along those lines. The way that they will integrate Altair into the next game/games is because Desmond had been exposed to the Animus too long, and therefore "became", per say, Altair.
Ha, there, I'm done, Woo for JIMMY!!!
James Isaac Hatfield
Merci Pour Le Venin, Et Les Lamus
What? Say something! Am I so beautiful that you're at a loss for words?-Midna, Legend of Zelda: Twilight Princess