Deus Ex was a genre defining, superbly designed and absorbing game that absolutely rocked my gaming world when I first played it. The story was far bigger and more open than in any previous first person shooter, the augmentation and skill systems were revolutionary, and the game world was crammed with interesting and useful characters, and huge amounts of information, making it one of the most replayable games ever (I personally played through it at least 6 times, and found new things every time). So Deus Ex: Invisible War was always going to struggle to match its predecessor.
First, the bad points - the AI is poor, and not up to the current high standard, although the AI in Deus Ex was generally woeful (one of it's weakest points), and Invisible War is certainly an improvement. The graphics are quite good, but again they do not hold up favourably against other current titles. The game world doesn't seem quite so rich - there are no newspapers lying around, or emails to hack from computers, and this is a sad loss from the original. The soundtrack isn't as memorable as that in Deus Ex either, and some of the voice acting is a little bland (although there are none of the truly terrible voices that occasionally appeared in the original - Hong Kong). Your character Alex D, isn't as charismatic as JC Denton, and ultimately you just don't care as much about him or her.
However, this is ultimately a very good game, and there are substantial improvements in some areas. The greatest strength of Deus Ex was it's freeform gameplay, and this is just as good, although different, in Invisible War - at times there are literally half a dozen ways to complete even a simple objective, and the only limits seem to be your imagination and the equipment you happen to be carrying- excellent. Some very fundamental changes are evident in the skills and augmentation systems too - biomod canisters can be installed in one of 5 slots, each of which corresponds to an area of the body, and can hold either an official or black market biomod. The abilities they give tend to influence your style of play far more than in Deus Ex, and this is a good thing in my opinion, although some may not agree.
The plot is a little loose at the beginning, but progresses smoothly, and with great realism. There is a real sense of freedom in your actions, and no matter what you do, the game has been designed to react accurately, and characters will often refer back to decisions you made several levels ago - this is impressive and creates a real sense of cause and effect. There are dozens of missions which are not crucial to the story, but carry rewards of equipment, money or information, and these seem a natural part of the game, rather than a tacked on extra.