I think one of the biggest reasons it is bashed so much on a gaming point of view is the fact that the game starts off with a reasonably free-form approach to an otherwise linear experience, and then transcends into something not quite as good.
As has been mentioned in posts above by commandercup, there are a variety of ways in which to achieve an outcome. Typically, you have a group of koreans, in a command post, village, road block etc, and you can frequently dictate how you're going to approach, (stealthly, all guns blazing, snipe and cover, or a personal favourite, run into one of the many metal trailers making lots of noise, then watch as the AI runs haplessly between the doors making for an easy kill, etc).
In fact if you simply go from A to B in the game, you miss out huge chunks of the island. Exploring wont reward you with more missions, conversation, or anything more than simply the fact that it shows a depth that many FPS's simply don't attain, (or at least, thats the principle, personally I've found the game begins to reiterate in what you can do reasonably soon into the game, and even on delta you can simply shoot and blast your way through the majority of the sections, but there is stuff to do outside the basic objectives).
But the biggest reason its often slated (which I am getting to
) is the fact that given this freeform approach initially, you suddenly (SPOILER ALERT) find yourself admist aliens in horrible even-more-linear-than-before sections of the game, with a quite frankly horrible "labyrinth" level in an anti-gravity section which serves no purpose other than to really annoy the player. Its a change of pace to the game which isn't a particulalry good one, and sees you having to play rubbishy scenarios like "protect your friend" and "mounted gun on the back of a jeep", which again takes away from what Crysis is trying to achieve (IMHO).
In addition, I found the game to be far too short, and obviously it has performance issues, though I have just upgraded to a 64-bit OS and have noticed a considerable increase in performance using the 64-bit Crysis.
Saying all that, however, its still worth getting the game to play through, even if its just borrowing it off a friend or waiting till it goes budget.