Rah rah rah PC gaming and all that, but I prefer Bioshock to SS2.
Better atmosphere, I think the game works better with a stronger emphasis on combat over RPG stuff, no weapon degradation.
I do miss the exploration, and Shodan was a more interesting bad guy.
But, while they both have atrocious, hilarious boss fights, Bioshock's is just a little less atrociously hilarious.
I think my draw literally dropped when I first saw the boss of SS2. I just couldn't believe I was chasing Shodan around some sort of merry-go-round, lobbing grenades at her.