The problem with Invisible War was that pretty much everything it did, the original Deus Ex did better. DX had bigger maps, more maps, more detailed damage modelling, more extensive weapon upgrading, better weapon implementation (aiming reticle, multiple ammo types, reloading), more detailed data vault, more detailed hacking (passwords, timeout zapping), more inventory slots, more aug types, more memorable characters, an experience system, better management of load zones, a less intrusive HUD, leaning, swimming, a control scheme designed around mouse+keyboard instead of a gamepad, and better graphics and physics.
Yeah, that's right-- better graphics and physics.
Graphics: Sure IW had higher polygon counts and neato shader effects, but the razor-edged dynamic shadows look like crap compared to soft-edged static shadows, the texture compression makes even high-res textures look distorted, the X-Box RAM limited them to a small variety of textures, they lost basic rendering features like damage decals, detail textures, cloud decks, and mirrors, and frankly the art direction and character design suck.
Physics: With the Havok physics engine, IW should have had superior physics, but they used it so badly that the end result is laughable. You can toss a body ten feet in the air, then shoot it straight up until it disappears from sight. You can accidently send a barrel flying across the room by bumping into it. DX's physics may have been primitive, but at least they weren't so obviously wrong.
Some of IW's problems can be blamed on the X-Box, but the sad truth is that a lot of its problems were fundamental design decisions-- like the meaningless faction system, cartoonish physics, or the whole "I can do whatever I want without meaningful consequence... therefore nothing I do matters" narrative structure.
