I had written out a lot of text here explaining why FO3 fell just short for me, and detailing why it's not because I'm an oldschool fanboy, but it had far surpassed TLDR dimensions so the summary is this: Fallout 3 spread itself over too much ground, trying to be too many things and drawing from too many genres. The only thing it truly excelled in was exploration, so when that's the type of thing I was interested in doing I'd play Fallout 3. If what I wanted was a good shooter, a good story, or a better roleplaying game, I'd find something else to play. Left 4 Dead, Neverwinter Nights 2, Mass Effect... whatever else I had on the menu at the time. And ultimately I went back to Oblivion for exploration, so another strike against FO3.
Fallout and Fallout 2 never had that problem, they were so unlike anything else (and so much better than the rare few they did resemble) that I never thought, "Hmmm... I'd like to kill a bunch of bad guys tonight, in spectacularly violent fashion... Fallout, or Duke3D?" It was Fallout every time. Duke3D was great at what it did, but it wouldn't let me sneak into a room, smash a mercenary's head in with a sledgehammer, and then shoot his buddy through the eye with a .38 magnum revolver. I think Bethesda made a great effort trying to keep that possibility in what is otherwise a more FPS type of combat system, I think VATS was a brilliant way to mix up the otherwise straight shooty-bang gameplay, but as with many firsts, it didn't quite make it. After a year and a half, the only thing that draws me back to FO3 is VATS. I keep trying to figure out how to make it work better in the next one.
Look at that, TLDR anyway. Well at least it's half the size this time.