The second one is definitely the best of the series. It's far less linear, a lot more diverse, and they fixed many of the mechanics issues that plagued the first of the series. The story line is also far more interesting as well as in depth.
I played AC2, all the way through, three times because I liked it so much.
One thing I like a lot about brotherhood is that it gives you the option to replay memory sequences, which AC2 and Assassin's Creed did not give you the option to do.