I played through system shock 2 as well, and as far as scaryness goes, IMO they're on the same level. System Shock has a setting of terror that I found to be even better than doom3 (the Many are really your worst nightmare), but the lighting of doom3 is so terrifying that I'd be amazed if system shock 2 would scare me as much as it did back then. I mean, that game should be a sunny day in the park now.
Furthermore, what's with all the complaining about the spawning enemies? That happened to me in System Shock 2 all the time! I just knew that after I'd cleared a room, some bugger would start running at me from just that direction. After some time it got predictable, you just knew when to expect someone.