Hmmm... Bioshock... I loved the graphics, the sound, the atmosphere. At times it had a genuine atmosphere of horror about it - I can still recall the lady with praying-mantis arms at the beginning of the first level, nursing her dead child... Unfortunately, in gameplay terms, it's nowhere close to System Shock 2, which is in turn nowhere close to the original System Shock. The difference is that the System Shock games had me hooked enough to keep going back to them again and again. Bioshock? Not a chance. The enemies, when they're not in their "horror" states, are quite boring. Who remembers the individual splicers anyway? I think Bioshock is a superb game engine and a good experiment in user-environment interaction. Now someone should make a great game out of it.
I would have to agree with everyone who's said SHODAN for best villain. In System Shock, SHODAN is the ultimate control freak, someone with the vision and power to play God on a grand scale. But in the sequel they develop this further and go with the theme of Shodan as a "mother" - awbeit one who is at war with her children. Nonetheless, when you destroy the last life-raft with the alien eggs in it on the Command deck, her gleeful scream of "You've murdered their children!" sends chills up my spine.
But there's a big objection: why in hell's name did they make the SS2 final boss a bloody cyberguard - one of the easiest cyberspace opponents from SS1? THIS is supposed to be the face of SHODAN? What a colossal let-down...