Oh yes, I agree with you that it was a really good ending, but that doesn't stop the questions from plaguing me xD Can't wait to see what happens in the next game. -nods-
The issue of whether the two guys were Abstergo or Assassin isn't really my main wonder, it is more that after the credits it briefly went back to the final shot at the temple before we're brought back to Ezio. It might have been a game mechanism that had nothing to do with interpretation or story. It really seemed strange to me that they would put Desmond back in the Animus when he's going through shock, but there might a justification for that I'm not thinking of. I believe the exact quote was "back into the Animus" which could semantically mean a number of things...like Desmond (if it is Desmond, dun dun DUN!) being in the Animus the whole time, even at the temple. Does that sound too farfetched?
What is your opinion on Lucy? There are so many signs that possibly indicate she is not to be trusted and I've been paranoid for one reason or another that she may be Templar.