This game gets kind of a bad rap, and it's easy to see why. For one, it's a sequel to one of the most heavily lauded games ever made. That automatically put it in the position of trying to live up to a nigh-impossible standard. But the game isn't bad, it's just very average. That's it's biggest problem, really: It's an average game that's a sequel to an amazing one. (Well, that and the stupid cover with the guy holding a pistol sideways.)
Invisible War takes place about twenty years after Deus Ex. Events at the end of that game triggered something called "The Collapse", which basically crippled civilization and caused a wide variety of problems that people are still recovering from. In a way, the game implies that all three endings from DX1 sort-of happened: J.C. Denton attempted to merge with Helios but fails, which causes the global network to cease to function, which results in the downfall of national governments and the rise of "city-states". Some people have a problem with this, and while I'll certainly agree it could have been handled better, I'm not sure what people expected. Did they think that the developers would make three radically different settings depending on which ending you picked in the first game?
You play as Alex D, a nanoaugmented student in the Tarsus Academy. Of course, things aren't what they seem, and just as in the original Deus Ex, you have to uncover a conspiracy and puzzle out what's really going on.
The game plays out much as the original; you go from city to city performing missions, although in this game you get to choose whether you want to work for the Order (a religious group that springs up after the Collapse) or the World Trade Organization (which has more or less become the new version of the U.N. in this game). Which you choose does affect how the missions play out. However, it ultimately has no bearing on the way the game ends, which is another problem people have with it. I don't want to spoil the plot by explaining this, but I will say that I agree that the ultimate reveal is kind of dumb and renders a lot of your choices meaningless.
Another story element that some people complain about is how several characters from the first game return, but have radically different points of view than in the first game. However, this complaint seems rather naive to me. First of all, it's been twenty years. People change a lot over that period of time. But more importantly, the characters in question were all directly involved in the events that triggered the Collapse. If your ideals led to a catastrophic event causing untold amounts of death and devastation, don't you think that might change your outlook?
Gameplay-wise, the game is very similar to the original, but there are a few changes that were made to simplify things that ultimately work to the detriment of the game. The biomod system is less interesting, the level areas are smaller in order to accomodate the X-Box's memory limitations, but the worst change (and the one you will hear EVERYONE who plays this game ♥♥♥♥♥ about) is the ammunition system. In the original game (as in real life and in most FPSes), each weapon had its own ammunition, and in many cases a weapon had multiple ammo types you could choose between (for instance, shotguns had both buckshot and armor-piercing rounds). In this game, someone decided it would be a good idea to have every weapon use the same ammunition counter. The conceit is that the weapons are using nanomachines to build ammunition, and that your "ammo" is actually the raw material used to make bullets and whatnot. The biggest problem with this is that the amount of this material that you can carry is severely restricted, and heavy weapons take a huge amount of material to fire. If you, say, use a rocket launcher a few times, you may suddenly find yourself having no ammo for your pistol.
Like I said: Overall, it's not a terrible game; it's just not good, either.It's easy to see why, when they made a third game, they chose to make it a prequel. Even if this had been a great game, it's hard to see where the series could go from here. I think the only way we're ever going to get a Deus Ex game set after the first one is if they reboot the original first... which, depending on how it's done, could be pretty cool, actually.
If you're a fan of the original Deus Ex, I would recommend playing through Invisible War at least once to see for yourself what's good and what's bad about it.