Yeah, I'll admit, the main problem with it was the fact that the graphics slowed the game down, which isn't nearly as much of a issue now.
I suppose my main problem is that, exactly as you stated, Doom3 without pretty graphics wasn't much of a game. There were some good moments, I'll admit that, but when Doom came out, the whole 'FPS' scene was new, Doom 3 was just another FPS, but with a more famous name.
Edit : Though, in all honesty, I did enjoy playing it simply because it was Doom
Oddly enough, this always reminds me of a Terry Pratchett quote...
'Mankind has tried several ways to fight the Ultimate Evil, Prayer, Doing Good Deeds, Fasting etc, why did it take until Doom2 for someone to think of the double barreled shotgun?'