As a sequel to the original Deus Ex, Invisible War is weak, being inferior in most aspects. The levels are much smaller, the the levelling system is massively neutered (you can only upgrade augments, as opposed to additional skills) combat is weaker in many ways.
With that said however, Invisible War is actually a pretty good game when taken on its own merits. First off, the atmosphere is fantastic. Even though the worlds are way smaller than those of Deus Ex 1, Invisible war uses lighting, music, and visuals to great effect, resulting in a moody world that draws you in, despite being so far removed from anything in the real world. The art direction is really fantastic. Furthermore, the storyline is really interesting. It doesn't start out quite as compelling as the original, but it picks up quickly and has loads of great twists. There were lots of memorable characters, as is series tradition, and it's great to see what became of certain characters from the first game (although I didn't care for what they did with JC Denton). Also, the fact that this game essentially provides closure for the Deus Ex Universe makes it very much worth seeing the game through to the ending.
One really interesting thing this game does that the first game didn't (and I'd even say Invisible War might be slightly better in this regard) is that you can actually choose which faction to work for during each mission. Invisible War carries on the first game's tradition of having your choices make a massive impact on how the story plays out (I've heard that your choice of character gender actually has an effect on some of what side-missions are available, but I haven't done a second playthrough so I'm not sure what extent this alters things to), and being able to choose who you work for brings this to a whole new level, as it lets you experience the story from different perspectives, and what you do at certain points in the game actually does effect which endings are available (as opposed to in the first and third game, where you essentially choose your ending at the last minute). How you interact with characters is key and your relationships with the characters can affect the gameplay in numerous ways. The dialogue plays out more naturally than in the first game (I do miss how all the random NPCs seemingly had PHD's in philosophy in the first game, as it was cheesy, but also really interesting and part of the original's charm) and the story covers some interesting topics. Interestingly, this game goes into a lot of the same pro-augmentation vs anti-augmentation debates that characters in Human Revolution had (this topic was in Deus Ex 1 a bit, but not to the extent of this game and HR), so it does seem to have at least had some influence on future installments of the series. Overall, the storyline is definitely a strong point, and worthy of the Deus Ex name.
Now, about the gameplay. Yes, it isn't nearly as good as Deus Ex 1, but it's still better than many games. Whereas the original was an RPG played through the interface of a first person shooter, this game is more of a first-person shooter with light RPG elements. Overall the guns feel decent (although the pistol is pretty useless), but the melee attacks lack punch. You'll be progressing through a series of cramped, but surprisingly non-linear levels and are given the freedom to choose your objectives based on what faction you like. There are a surprising amount of side missions, and just like in the original game, you can opt to do a pacifist run. Your augmentations can let you do some crazy, almost game-breaking stuff (Bot Domination is particularly awesome. It lets you take control of enemy robots, and getting the jump on an enemy patrol who was hanging out with enemy robots is both awesome and hilarious), which can lead to some fun situations. Something that's interesting about how this game handles augments is that you can actually replace your augments with a different ones if you find yourself in a desperate situation where an augment you didn't choose would be helpful. This is a last-ditch strategy though, as the new augment starts out un-upgraded, so you'll usually have to carefully weigh your options. Unfortunately, the weight of this decision is lessened a great deal by the sheer abundance of upgrade cannisters in the game. By the time you finish, you'll probably have at least 10 or so extra cannisters laying around, meaning that if you swap augs for a situation, you can often easily swap back to what you had before and re-upgrade it to the maximum level. Swapping is still an interesting and useful mechanic, even though the abundance of upgrades hurts the design.
The inventory system is a bit awkward. You can only carry somewhat small amount of things, which makes sense from the standpoint that the developers want you to pick and choose a playstyle, but gets frustrating when you just want to pick up a medkit and all of your slots are full. Not too bad, but it does add up over time. Furthermore, there's a bug where sometimes more than one of the same item won't stack, which is especially frustrating for the lockpick multitools, as some doors need a certain amount (so if a door needs four tools, and you have two stacks of two, it won't open), which is incredibly frustrating. The interface of it is also a bit clunky, being clearly designed for a gamepad. It's not offensively bad, but moving an item to be equipped is a bit tedious, as you can't click and drag. Instead, you click the space for the item you want to move, and then click which slot you want it to go to.
The main flaw of the gameplay is the universal ammo system. Basically there's one type of ammo, and if you run out of it for one gun, you're out of luck for all of your guns. It's frustrating and you run out often, but there are some benefits. It does force you to use stealth in some places and it encourages an efficient style of play (always go for headshots if you can). It also leads to some tense situations (such as you versus 15 armored guys and some robots with little ammo) that force you to think way outside the box and come up with your own solutions to problems, and it was actually during these parts that the game felt the most like Deus Ex 1. Despite these interesting situations, Universal ammo is a pretty ham-handed way of of making these things happen, and the same effects could have been achieved in different ways with better design. For all the neat gameplay scenarios it causes, it also causes a noticeable amount of annoyance (although there's always some way out of your problem).
The level design is solid (despite levels being really small) and it does encourage you to expore the environment. You still have multiple ways to do things and what you do has a fascinating imact on the story. The real problem with the levels is that they're split up into many separate maps, which means you'll be seeing loading screens a ton. This isn't too bad as today's computers can load things rather quickly, but for some reason the game minimizes to the desktop each time a map loads, and then goes back to normal once everything is up. This is jarring and does take you out of the game abit, so an actual loading screen would have been nice. The levels themseles are densly packed with detail, and there is a great variety to the environments you'll be in. Most levels have a nice kind of back and forth flow, almost reminiscent in some ways of the level design in an oldschool Doom game (in a good way). The game mostly takes place in interiors as opposed to the large outdoors environments of Deus Ex 1, but the levels aren't bad.
Overall, Invisible War falls short in many areas, especially compared to the original Deus Ex, but taken on its own it is a very interesting game that's definitely worth playing. There are a lot of unique ideas, and even though they don't all pan out, it mostly falls on the "good" side of things. Recommended.