Don't get me wrong, both games are amazing and revolutionary. In terms of gameplay, quests, smoothness of game, weapons, etc, FNV is better. But, the reason FO3 is overall better is simple: the atmosphere. The music in FO3 is amazing. Either very happy or very sad and it gets you emotional when you are wandering the hopeless, desolate, bleak Capital Wasteland. The music in FNV isn't bad, you can't go wrong with Frank Sinatra or any of the songs, but they aren't Fallout-y, if that makes sense. They are more positive, western songs. Also, FNV seems too rebuilt. And what I mean by that is sure there are problems in the Mojave, but overall, society is somewhat civilized now and rebuilt almost; big cities, big factions, etc. FO3 like defined the definition of a post-apocalyptic world. Unimaginable atrocities, desolate land with limited establishments, seemingly overrun by animals and enemies, not overrun by a government force, NCR or a formidable evil society that is strong, Caesers Legion.
I don't know if my rambling make sense, but FO3 is better overall. FNV is brilliant, but it's not bleak enough and the music for sure doesn't make it feel bleak like in FO3. Into each life some rain must fall, way back home, etc those beat jingle jangle jingle and blue moon any day when it comes to Fallout atmosphere. FO3 and FNV are amazing, but FO3 is better thanks to the atmosphere. If FO4 ever comes out, I hope they make it like FO3 in the atmosphere aspect, but FNV in every other aspect.