The core gameplay has not changed much. The only real differences are in the fighting. In AC3, the fighting is more fast paced, and while you can still counter attack and just kill every one without taking any damage, it is much more difficult, mainly because the enemies are more aggresive.

I feel that the pacing of the game is different. While this is not a bad thing, I dont think that it is a good thing either. The story makes a bunch of leaps in the time line of Connors story, but also, I dont feel like i am as free to do what I want "early" in the game by early I mean a third of the way through the game. Normally in the other installments of Assassins Creed, you could do what ever you wanted to instantly, while in this one, the world seems limited, and you as the player are pushed to do the story very quickly. This doesnt make me mad, i just dont want to be guilt tripped into playing through the story, and then not exploring.
I have found some minor bugs, NPCs dissappearing, or NPCs not following. All of these bugs were fixed by simply reloading a check point, but its still irritating when something like that happens.