Well it looks like this was something that Ubisoft wanted to address when making the sequel, in title only. In fact, below is a nice video showing how there are going to be so many new mission types and events in the game. Including parts where the game's NPCs will fuck with you just because you are there. On a mission or not. Example:

You could be on a mission to assassinate, steal, or whatever to progress the story. While tracking your mark, the town's pick pocket runs up and snags your money bag and runs. You can choose to hunt him down and reclaim your money, but this could lead to failing a mission or just a minor inconvenience. It's your choice.

Kind of a cool little addition to the game. Not to mention events that take place during cut scenes that can effect the outcome of the scene. To quote the video, "You could take an action that will end the scene with you hugging a lady. Or if timed right something much 'different'."

Awesome steps guys. It always makes me warm and fuzzy when developers listen to the gripes of us gamers.