Fallout 3 is much better for replayability.
New Vegas is good for 1 good and 1 evil play through, the only differences come near the ending, for the most part you're always going to go the same route.
world.
I think you got those messed up, you only got Good, Evil, or Neutral in FO3, but the quest (singular) was pretty much the same, in FNV you have Good NCR, Bad NCR, Neutral NCR, Good Legion (Hard to do), Bad Legion (Surprisingly easy), Neutral Legion, Bad House, Good House, Neutral House, Good Independant, Bad Independent, Neutral Independant, and the NCR/Legion/House/Independant all have different interactions and even different quests, the similarities are do to logic, what power-vying faction wouldnt want to garner support from minor factions?
In FO3 I just ignore the main quest but in NV you can't do that, the quests are the meat and potatoes of the game.
As is proper in an RPG.