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.
I'm a heathen on this board. I haven't played FO1 or FO2. I just got FONV, and decided to buy FO3 at the same time. So, this is from a total lore noob, keep this in mind if you want to dismiss what I'm going to say out of hand. Blame my heathenness and noobyness... but I prefer FO3 over FONV - and I'm basically playing them concurrently.
In FO3 I stepped out of Vault 101, got blinded, and as my vision cleared I looked out over the devastation below and was awestruck. Such devastation. Admittedly, it was my first contact with the world of Fallout. GNR was just static. Enclave radio was suspiciously gregarious. A few mole rats subsequently feasted on my carcass outside of Megaton. I loved it. Twenty hours or so later, I'm about to start getting serious with the main quest because I keep getting sidetracked by mini-quests. Whether it's to sneak into mirelurk nests and plant stuff, shivering over the messages in the computers in Georgetown, wondering about who Grady was and why he was handling the naughty nightgown.
I love FONV too. But I'm not really getting sidetracked from the main quest. I haven't met this bratty kid running up to me complaining about ants yet in FONV and demanding I solve it NOW. I've just devastated Caesar's legion in the east, but couldn't finish the job because there was two brats in the Fort that were immortal. Yes, the Legion breeds immortal kids. In FO3 I got an earful of four letter words from a kid about half my length. FONV is more like a train track you're on, more like a theme park where you're guided toward an end. I haven't really stopped to wonder about any of the people here. They don't have that extra dimension of mystery about them. They're actors working for a singular end for their factions. I can't really put it clearer than that.
These are, as I said, my impressions of the game. I can spend a lot of time in FO3 just following a dungeon to its end to find computers to hack to find out more about it. I don't tend to do that in FONV. I don't really know why, and it is of course HIGHLY subjective of me to say that.
I read the other threads about this stuff, and scratched my head. People have painted themselves into rhetorical corners about this subject, it seems, and are digging up details to support their viewpoint. For me, and again it's subjective, FO3 is more of a world while FONV is more of an adventure.
/rambling end.