Weird.
My FPS got a lot better after I got initiated into the assassins. I even put my graphic settings higher, textures to the best and environment graphics to Very High, even though I've got GTX 680 (minimum requirement according to Ubisoft..).
FPS was shit at first, in the prison and prisonbreak.
Oh yeah, and, I do like the game more than any other AC game so far. It's a money grab, and it could be really, really good if Ubisoft wasn't so greedy and gay, but it's decent as-is. Definitely better than previous installations, IMO.