They are both good games, but they are different styles.
FO:NV is all about the complex quest interaction between the opposing factions.
FO3 is all about exploring the wide open world. Yes, there are quests, but they're really just something to do in that world. FO3 also feels alot more "post-apocalypse" since civilization in that area is less recovered and there's alot more major ruins all over.
Beyond that.... well, FO:NV's game mechanics are a bit better, since they were tweaked from FO3's. So in that sense, FO3 will be a bit of a step back.
But it's still a good game.