Invisible War's biggest sins were:
1. Having to follow up the first game, which was a masterpiece
2. The universal ammo pool, which made most of the weapons entirely pointless
3. Primary target for the game was the Xbox, which made the levels much smaller and forced more loading screens
It wasn't as irredeemably bad, but compared to its predecessor it was a disappointment. And with the release of Deus Ex: The Fall, there's now a game that's demonstrably terrible to point at as the worst in the series.
Also echoing with the choir, it sucks that they're not going to wrap up Jensen's storyline so we can move on to other parts of the universe.