I think what killed Doom 3 for me was the pacing. In Doom and Doom 2, you were constantly assaulted from all sides - I mean, the battle was to stay alive to make it to the switch.
In Doom 3, you fight a few demons, and then go wonder around in the dark awhile, blasting the occasional imp that is hiding around the corner. Are you kidding? This is supposed to be Doom, not Resident Evil. I mean, the game had like 3 cacodemons. How many pinkys? Maybe a few. There were more pinkys and cacodemons in a single level in Doom than there are in the entire game of Doom 3. That just isn't right. In Doom, it was blast blast blast all the way, baby. In Doom 3, it was let's listen to retarded audio tapes with horrendous voiceovers. Once you got to hell it got a lot better. But the first half of that game killed it for me. It was also way to easy - except on nightmare, where it was impossible (ever decreasing health, are you serious?). I mean, I basically rode the quick save and quick load buttons the entire time on nightmare, and to the point that it wasn't so much a challenge as it was an excercise in trial and error.
As a whole, Doom 3 reeks of bad design choices and poorly implemented ideas. I did think ROE was much better, though.