I agree with you!  AC2 was the best.  It had a great all round story and the puzzles and dungeons were interesting and fun.  And, let's not forget about all that beautiful Italian architecture.

Ezio and Altair were great characters.  They had personality, charm and dynamic with other characters that made you want to flip through the chapters of their stories.  That is why starting off with Haytham was so appealing.  His approach and demeanor is familiar to what we are used to with Ezio and Altair.  His character reminded us of the allure of playing a character that carried out missions with stealth and precision.  We liked him and established an early respect for him, even though we all found out who he was.

That is why a big part of me believes that Ubisoft deliberately tried to make Connor a different kind of character and assassin.  Unlike his predecessors, there's nothing romantic about him.  His cause is as generic as any, and with how it was introduced in the game, I found it hard to immediately support, sympathize or relate to him as a protagonist.

There are times where I find that I had to will myself to stay in the animus and I looked forward to the times when I didn't have to be.  Having such a flat main character made me feel like I'm playing the game just to go through the motion of completing tasks, as opposed to achieving objectives to further the storyline.