The end is really, really good, and ties a lot of things together.
I enjoyed the Altair sequences. The rest... the story was just too short. I mean, I realize they had over 3m people playing multiplayer, but, still... most of us bought the game for the Ezio storyline.
If you're looking to 100% the game, you have to do a lot of different things that aren't required in the actual gameplay.
One thing I was disappointed with in comparison to Brotherhood - only one side mission per faction (thieves, Romani, mercenaries). There were at least 5 each in the last game, and they were in AC II, too.