I liked Fallout 3 a bit more, though that might be nostalgia. New Vegas, while fun, just doesn't... mesh. The storyline and tone doesn't seem to fit together at parts (you start out tracking people down and making them pay, but end up as a key soldier and diplomat in a war between two factions, Old World Blues is basically everything the main game wasn't in terms of tone and story, this is post apocalyptic, but almost everything is intact, ect.), the weapons don't seem to match (starter weapons are low-tech weapons like lever-action rifles and revolver pistols, but late and even mid game weapons are high-tech plasma cannons and M16s), and the characters just don't really fit (are they supposed to be survivalists holding on after the end, cowboys forming a new life, gangsters, or pioneers on virgin soil of new land for an empire?).
Meanwhile, despite some hick-ups with the BoS, Fallout 3 fits most of the time. Tech-level stays high throughout, the entire storyline is still revenge (this can be an interpretation of why you went looking for your father), and the characters, spare a few, are all survivalists. The only exceptions would be Rivet City (who are still only barely beyond survival, nowhere near like Caesar's Legion or the NCR), the Brotherhood of Steel (who are like this everywhere), and a few scattered towns (most of which you have to save from some threat). Plus, you can believe this was the end of the world. Skeletons everywhere, places where large firefights were, destroyed cars, ruined cities, common pockets of radiation, everything made it seem like things had actually ended. I just didn't really... get that with New Vegas. I still love both, and I can't wait for Lonesome Road, but I think Fallout 3 just achieved more of what it was trying to be.