System Shock 2 IMO was FAR better at atmosphere than Bioshock. Bioshock has some spots that make you jump, but all in all, I didnt feel a PART of the world, especially when there is disconnecting events, such as early in the game, getting the first plasmid...
Why would I, a stranded person fresh from a plane crash, finding a strange needle thing, without even QUESTIONING wtf it is, just straight up inject myself with it? Im sorry, but that ripped me out of the game faster than anything else Ive experienced before (in a FP game).
I think so many people are saying Bioshock simply because, in the scheme of things, they are new to gaming, and when your game experience is limited to pretty much the past 5-6 years, well, your perceptions of what makes a good game is (IMO) a bit skewed.