There's been loads of topics of how great SS2 is, how it's the best thing ever and how there has never been a better horror game. By now, there's a lot of hype surrouding the game, a lot of misconceptions, and I believe that some people will turn out to be disappointed when they compare what they've been told about the game and the actual experience: And this is a topic for those people, or to warn others of issues this game has (and it does have quite a few.)

Let's start by the misconcetions, stuff that people say and I believe it's simply not true:
1) System Shock 2 is an RPG
Nope. No way. SS2 has stats and skills, but building your character correctly is not crucial to your success (you can mostly just take whatever and still get trough the game) and your skill as FPS player will be much more important. There are also absolutely no story-based decisions that would be important for the game in any way, shape or form - at best SS2 is a game with some RPG elements. I'm posting this as a warning, and I'm not willing to discuss it - if what I have described above fits your definition of an RPG perfectly, go ahead and think of SS2 that way.

If you don't mind what I have mentioned / just want a second opinion, look over here.

2) System Shock 2 is the best horror game evah, and so difficult!
First bit is very subjective. Some people are very afraid while playing SS, some aren't - most of the horror and difficulty are tightly tied together however, and the moment you get more powerful arsenal, you won't be quite as scared. To explain what I mean: About 1 third of the game, if it is your first playtrough, you are most likely going to be genuinely scared. Resource scarcity and your inability to tell which skills are the best to take will make sure of that. But then you'll learn the game, learn the mechanics, and learn survive quite easily, which takes fear away and turns SS2 into a horror-themed FPS. A brilliant horror-themed FPS, but a horror-themed FPS nevertheless. Therefore, if you are looking for the scariest game you have ever played - SS2 probably won't be it. But the first third IS worth it alone, and the rest of the game is genuinely great as well.

Now, to the game itself:
1) Skills
There are some fundamental issues with balance in this games. There are skills which are flatout better than others, weapons which will easily outperform others etc. I won't go into details here, just - don't look for a Diablo 2 experience here, problems in this area will become apparent very quickly, which actually kinda adds to the survival element of the game ... Still, it's not really a good gameplay design, and it can lead to artificial difficulty.

*KINDA SPOILERS IN 2)*
2) Quality degradation
The game feels rushed towards the end - levels get a lot more linear and a looot less interesting, if I don't count a ... Particular ending bit which is linear but kind of awesome. And I always felt that the boss battle really, really sucked, altho what led to ... her was fucking amazing as a throwback to the first game. I'm getting distracted tho - as you get out of the first ship, game suddenly gets a lot less interesting and a lot more FPS-y.

These two points aren't criticism per se, they're just annnoying for some people:

3) Inventory tetris
Some people don't quite find this to be a problem, others care a lot, sp: Inventory management in the game is done via limited grid, in which you have to place equipment of varying size.

4) Respawning enemies
While enemies never respawn 'completely', as in you will never have to fight the same hordes that you have killed the first time in an area, one or two will always spawn from time to time (or more if you trigger an alarm).

Well, that's my two cents. It's really not much, which shows how much I actually enjoyed the game, altho I will eventually come up with more - feel free to discuss and add your own, if I see a well-described argument, I'll edit it here, into the OP.