New Vegas, no question. It did almost everything better than Fallout 3. Only thing it completely failed at was interior design.
Seriously, even 2 room houses were fucking labyrinths. And I was scared of entering vaults solely because I was afraid I would get lost in the place and get eaten by a minotaur.
But yeah, story, world, characters, writing, companions, gameplay(you no longer have to rely on V.A.T.S. for every god damn encounter, and 3rd person is now a decent gameplay choice)... everything is much better than Fallout 3.
Also, New Vegas has Wild Wasteland, which is the greatest trait ever.