Yep, AC2 is tops in the series.
The frustrating thing about the AC series is that it seems that every new title has at least one killer feature that the others don't, but is lacking in other areas. AC2 had the best setting and most interesting cities. ACB introduced the assassin recruits, an awesome new feature. ACR had the tower defense thingy (ok, that sucked). And AC3 had the frontier, naval battles, and IMO the best story of the series. But the cities were small and bland, the new monetary system was needlessly complicated, and Desmond's ending (I've never cared for this element of the series anyway) was simply a joke.
I'm still waiting for an AC title that manages to put it ALL together. Maybe Black Flag will be the one. Because if they can pull that off, it can be one of, if not THE greatest game ever made.