Might be controversial, but the first game for me will always be my favourite. I'm not saying it was the best, but just my favourite. I still remember the announcement trailer and first gameplay being shown. A third person medieval assassin game where you could climb buildings and every nook and window sill was just crazy and really looked like it was pushing boundaries. I was basically frothing at the mouth with excitement. Also unlike the new games, back then you didn't fly up the side of buildings. Everything took a while and it looked difficult, i kind of liked that grounded feel although for the sake of gameplay i'm perfectly happy now to have it sped up.
The difference in the feel of Acre or Jerusalem was pretty well cool, even if a large part of it was a colour filter. I still have a soft spot for that game trying out something new.