Man; that ending was great, however crazy it maybe. Saying that, here is my equally crazy theory behind both the ending and the credits voice-over:

So, what if the whole of AC 2 takes place within another animus and its Desmond’s son currently in it.

It goes some way to explaining the two unidentified voices over the credits and their conversation. I mean what son wouldn’t have a heart attack when re-living the point where dad was forced to stab their (maybe) mother.

Maybe I’ve watched Inception to much... I’m not sure.

I don't remember who said this or if I just think someone said this already but. I think it might very well be still desmond only it's after 2012 and he is unknowingly going through his memories trying to figure out what desmond did with the apple after he killed lucy. Much like what happens when Desmond tries to relive a traumatic memory in the animus they have been forced to have desmond go through memories further in his past so that they can actually relive the memories they are searching for. The memories being what happened to Desmond, Rebecca, and Shaun after he was forced to kill lucy.

I'm still not convinced Lucy is really dead.

" I'm still not convinced Lucy is really dead. "

" @papercut said:

" I'm still not convinced Lucy is really dead. "

She got stabbed, if their were any ambiguity, it would have been clearer. One theroy  that i've heard is that Desmond is Adam and Lucy is Eve. Eve has to be punished for her wrongdoings so whenever this happens, the eve must die, Lucy "

I was under the impression that the voices on the credits was a reference to Subject 16  ("But the animus did this to him") and foreshadowing for what may happen to Desmond Psychologically. Also I thought that the implication of Desmond stabbing Lucy was that the "gods" are displeased by the Templar/Assassin wars and they were going to make Desmond their agent for ending it, at the cost of humanity if necessary.

I'm pretty sure the voices in the credits were two men dragging Desmond (you can hear him say "No..") back to the Animus as just somewhere to put him for safe-keeping while they can figure out what to do next. Note that you can no longer select "Leave Animus" after the game ends. 
 
The real question is who the men are. More assassins? Templars?

This has been the theory that has been passed around, and I'm still not really convinced by it. I think it's a bit too obvious. 
 
@Haru48 said:

"Also I thought that the implication of Desmond stabbing Lucy was that the "gods" are displeased by the Templar/Assassin wars and they were going to make Desmond their agent for ending it, at the cost of humanity if necessary. "