Might get killed for saying that, but I actually never understood why it has been hated that much. Sure, it was far from being a masterpiece, but it wasn't THAT disappointing either. It was a commercial failure more than a creative failure, in my mind.
Sure, more was promised, than what we received, but well. Many decent games suffered the same industry treatment, even Fable and Black & White.
As for the setting, the complaint I kept hearing was that it was "too sci fi", but in the end, really ? Except for the Omars, I can't remember anything that doesn't fit in the established lore (held by only ONE previous title, as Irwin said. Nothing like Fallout, in my mind). There has always been cheesy stuff in Deus Ex, Illuminatis, aliens, sci fi, bionics, holograms, zealots, unbelievable artificial intelligences acting like Dr.Evil and clones in the established setting. Even anime weirdozoids like energy katanas and bionic Yakuzas. In the end, I don't really see how Invisible War raped the franchise. I didn't like the templars factions, but there has always been that weird faction in Deus Ex. Remember when you go to Paris, and the Majestic 12 guys (supposed to be ultra secretive, a force that isn't supposed to show itself) patrol the streets in full power armor, heavy weapons in hands, and nobody bats an eye ?
Even the idea behind the Omars is pretty decent, I think. The concept of cheating your way through black market, illegal bionics, with all the risks it implies, is a nice addition to the existing gameplay. Hell, even the next, next gen Deus Ex acknowledges Invisible War as part of the lore, judging by the first prototypes of technologies here and there, the very ones you also have in Invisible War.
Keep in mind that I played it years ago, and my memory isn't fresh. I just remember that I didn't understand why it has been so widely hated, but I may forget many things.
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