1. The Enemies: It's so annoying when majority of them can kill you with a single hit and when they die, another one respawn right behind you and kill you before you could even react. I absolutely hate the cyborg ninjas and spiders because they take so many hits before they hit the ground.
   
2. The Maps: I find the navigation in System Shock 2 to be so laborous and tiresome. Half the time I have no idea where to go and what to do. The mission objectives tell you to go somewhere but when you look at the map, you can't find it anywhere. For example, the objective tells me to head to the bridge but when I look at the map, I don't see any bridge. Then I wandered around aimlessly looking for this bridge but I still can't find it. About like an hour later, I finally found the bridge but it wasn't a London Bridge kinda bridge but a Command Center kinda bridge. That is so freakin' misleading!
   
3. The Weapons: When it comes to an FPS game, your weapons are your friends and when you don't have them, you're screwed. In System Shock 2, you can find  weapons lying around everywhere but when actually want to use them, it's either broken or jammed so you have to fixed them. It's a cool mechanic but the problem is is that the weapons are so fragile it becomes busted very easily after only a few shots. It's especially stupid when your weapon goes kaput in the heat of a battle and when you wanna switch weapons, it might be too late.

1. The Enemies: It's so annoying when majority of them can kill you with a single hit and when they die, another one respawn right behind you and kill you before you could even react. I absolutely hate the cyborg ninjas and spiders because they take so many hits before they hit the ground.
   
2. The Maps: I find the navigation in System Shock 2 to be so laborous and tiresome. Half the time I have no idea where to go and what to do. The mission objectives tell you to go somewhere but when you look at the map, you can't find it anywhere. For example, the objective tells me to head to the bridge but when I look at the map, I don't see any bridge. Then I wandered around aimlessly looking for this bridge but I still can't find it. About like an hour later, I finally found the bridge but it wasn't a London Bridge kinda bridge but a Command Center kinda bridge. That is so freakin' misleading!
   
3. The Weapons: When it comes to an FPS game, your weapons are your friends and when you don't have them, you're screwed. In System Shock 2, you can find  weapons lying around everywhere but when actually want to use them, it's either broken or jammed so you have to fixed them. It's a cool mechanic but the problem is is that the weapons are so fragile it becomes busted very easily after only a few shots. It's especially stupid when your weapon goes kaput in the heat of a battle and when you wanna switch weapons, it might be too late.

If you're talking about reviews from major publications then you have to remember that the game came out over 10 years ago and the gaming landscape has changed significantly since System Shock 2 was released.  As for for reviews that have been written more recently, only people who really liked the game are going to be reviewing it this long after it was released.  In regards to the difficulty, the game is really fucking hard, and the general trend of making games easier and more forgiving puts you in a far worse position then people playing it when it was released.

I honestly can't say I found this to be too hard. I bought this game in a triple pack years ago and I clearly remember getting in trouble off Mum when she busted me still playing at 4am the night after I first got it. 
That's not to say I didn't die but certainly no more than any other lengthy RPG. 
Eventually I played it through with a character from each speciality and as long as you play to the strengths of their background then you're avatar should be pretty beefy by the end. I recall the enemy I most feared were the Midwives with their nasty green lasers! 
You say in your review though that you were annoyed upon finishing the game because you couldn't make it easier for yourself by using an FAQ. Perhaps I come from a different era of gaming but I'd feel horribly disappointed in myself if I needed to refer to a walkthrough unless I was so stuck that I'd just stop playing. For me the sense of satisfaction in completing a game by your own merit is much more rewarding and you're generally given step by step instructions by Shodan as you move through this game anyway. 
The reason this often gets full scores in reviews though is because it was the precursor to so many things we now take for granted in video games and Shodan is an example of one of the greatest arch-nemesis ever. 
System Shock 2 remains one of my go to games when discussing my favourite games ever and while the game is generally credited to Irrational, it was such a shame that Looking Glass didn't survive to make more games like this.

its hard at first, but when you get used the the style of game it is then its not too bad. System Shock 2 is probably my favorite fps game....

With System Shock you have to realize that it's an traditional PC RPG that only looks like a first person shooter. You can't treat it like Call of Duty, everything you do has to be methodical. It also helps to pick a class and then only put modules into that class. So if you chose Navy, only put points in hacking and pistol. If you want to be easy you have to pick Marine and max out your strength and just one shot everyone with the wrench.

I thought system shock 2 was a rather easy game honestly.

I played through the game for the first time a few months ago, and on normal I'd say it's just the right difficulty. I played as Navy, mainly leveling up my tech skills, so I didn't have very heavy weaponry and never even touched a PSI Amp. I died a few times, I think, but that's about it. I didn't have many problems with guns either; I generally used them as a last resort when the enemy was too dangerous to kill with the wrench/crystal, such as the exploding robots or the spiders, because of their poison. I can't remember getting instakilled at all.
I found it very easy to navigate the Von Braun, the devs did a great job with leading the player on a linear path while still letting him explore the ship rather freely. This might be the sci-fi fan inside me, but seriously, of course the bridge would be the command center, it's a starship!

It really isn't that hard of a game once you get the hang of it....it does have a steep learning curve though,

WARNING: Wall of text imminent.