So I finally beat the first installment in what I'm going to refer to as "the Shock trilogy" (System Shock 2, Bioshock, Bioshock Infinite) and I have some thoughts on it. Most of them are positive! Some of them are not. You have been warned. (Oh, and spoilers for a 14 year old game.)
First off, let me be clear: I will not hold the graphics against the game, because that would be stupid. When I play an old game like this, Deus Ex, or Morrowind (all of which I've gone back and played through for the first time within the past few years), I try to hold it to the standards it should be held to at that time. It was released in 1999, and it looks pretty great when you consider that. Also, full disclosure, I downloaded a bunch of the mods on this list before even starting the game up, so I wasn't even playing with the original graphics.
So. Bioshock really took a lot from that game, huh? I had always heard that Bioshock was a spiritual successor to SS2, but, I mean, they play almost exactly the same and it has almost the same plot twist halfway through. (That you've been working for a second bad guy the whole time).
I really enjoyed SS2. The story was very good for a game released in 1999 (It was basically this, Half-Life, and Deus Ex that started the ball rolling for serious storytelling in video games, right?), the setting was fun, the Many made for a suitably creepy villain, and even all these years later I think it works really well as a horror game, to the point where I had to step away and take a break for a little bit while playing a few times, because I was freakin' out (Partly because of the spiders. Mostly because of the spiders. ...Yeah, I didn't like those spiders.).
That said, there are elements that really don't work for me, and if I had to rate them, even considering the time they were made, it would still have to be my least favorite of the Shock trilogy. To be honest, and I know that this may very well get me crucified by fans of the game, most of the things I liked about SS2, Bioshock did better.
First, the setting. The Von Braun is a fun setting, and I won't argue otherwise, but the reason it's fun is because, hey, space is fun! There really isn't anything special about the Von Braun as a setting, it's just a space ship like we've seen in dozens and dozens of other sci-fi stories. Now there's not anything wrong with that, but if you contrast that with something like Bioshock, and... Well, Bioshock is a truly unique setting. I've never seen another game, or for that matter a movie or book, with a setting that was even similar to Rapture. Everything about Rapture just oozed style, from the look of the city, to the time period it was set in, to the individual areas you visit.
Second, the sound design. Now, on the one hand, System Shock 2 has some excellent, very creepy sound design, that really makes it an effective horror game. On the other hand you have to go into the menu to turn off music to experience that, because the terrible techno music that plays during combat completely spoils the mood. The voice acting, with the exception of SHODAN and maaaaybe The Many, was terrible, but all video game voice acting in 1999 was terrible, so I'm not going to take marks off for that.
And finally, the last few hours. I think the last couple hours (pretty much the Rickenbacker on) are pretty poorly designed for one specific reason, they artificially increase the difficulty by just not giving you any more ammo. Now, admittedly, that did make the game harder, but that's not always a good thing. I got to the last section (Cyberspace), and I had 0 bullets. I could not defeat SHODAN. I had to go through the Body of the Many again with a previous save (which, by the way, is also a pain to get through because it all looks alike, and those gas leak things are just incredibly annoying) so that I could conserve enough ammo to even have a shot at fighting that boss. I don't care if it's 2013, 1999, or 1730, that is bad game design. There should be some, not a ton by any means, but some ammo between the incredibly difficult gauntlet at the end of BOTM, and the fight with SHODAN, especially considering that she is impossible to hit with the wrench/crystal. There's a difference between being hard, and being unfair, and those last few hours of System Shock 2 cross the line.
So yeah. It's a very good game, one which fans of Bioshock should totally still go back and play, but I don't think it's the "greatest game of all time." I don't even think it's better than Bioshock (which, let's be clear here, is far from a perfect game).
But seriously, I hate those spiders.