Really, the story jumped around a whole lot and contained too many parts with really no significance whatsoever. Gameplaywise it was an improvement, but there's still flaws. Like the levels where you're supposed to get to a certain point without being seen, you can literally shoot everyone with the crossbow and no one will get even the tiniest bit alert, even if you shoot the person right next to them. But there are parts where if you assassinate someone with the hidden blade and they see you right before they die, but it's still mission failure.
For the story, I don't really remember exacts because it wasn't that good, and definitely not as good as 2's. And the one level of Rome really pales in comparison to Florence and Venice and all the other little places you could go to.
Really, 2 was a better game in almost every regard.