I should point out that, I didn't play System Shock 2 myself till after I played Bioshock. That game did manage to disappoint me for the reasons I gave above which are reasons purely relating to Bioshock itself. The reasons for why it falls short of System Shock 2 are a bit more complex, and whilst maybe making a direct comparison is a little unfair, it would be even less fair for people not to try System Shock 2 at all.
I feel the comparison should be made because... putting it very bluntly and without the detail really needed, Bioshock's gameplay design was extremely dumbed down compared to what System Shock 2 offered. It wasn't as challenging, and it lacked a lot of the subtleties in SS2's gameplay. And whilst SS2 wasn't perfectly balanced by any means, it was at least a bit harder to essentially break.
I believe, honestly, that there is evidence here (and not just between these games, see Deus Ex 1 and 2 for even clearer example) that game design is being simplified because developers believe that is what gamers want, and if gamers continue to let them off by applauding games like Bioshock (which isn't like a bad game in the normal sense of the word but to really rate it highly requires ignoring some of the things that it falls short on) then we're not going to get games that focused more on delivering complex and challenging experiences.
I'm not saying this to try to sound all high and mighty, all I ask is you consider this, and compare these games and look at some of the patterns. It's by no mean prevalent in every game, because like say, Fallout 3 was definitely a game that tried to maintain as much complexity from it's predecessors as was practical. But for every game like that, well, you get Bioshock, which I feel without it's setting, would be very generic indeed.