I thought New Vegas had a more interesting story, I thought the factions were a great addition, companions were handled much better, the karma system was less black and white, the weapons and ammo systems had more depth.
The environment of FO3 was perhaps more interesting to explore outside of the goddamned tunnels, but I don't see how New Vegas was a worse game outside of the bugs (obviously). It isn't sequel-worthy by any means but the content of it as a stand alone game was great.