Well I've played FO3 and NV, but I'm also pretty well versed in the lore, so here's my take on it.
FO:3 and NV were both great games, but they also had very different strengths and weaknesses that reflected their different developers. FO3 had a bad story, mediocre characters, and generally fell down when it came to plot related stuff. But it absolutelly excelled in the actual gameworld. Compare this to NV, which had a great story to tell, but really lacked atmosphere.
I'll try and demonstrate through some examples. Compare the moments from the two games when you first stepped out into the wasteland. In FO3, after going through a hectic escape from the Vault, the door slid open with a huge sound of grinding and screaming metal. Then you walk down a tunnel, silent as the grave, with centuries old skeletons at your feet. Open the door at the end, and step out. It takes a moment for your eyes to adjust, and then the view hits you. Slowly walking up to the scenic lookout, you see the bone dry wastes, a ruined road littered with burnt out cars, a massive broken off overpass to your right. Further down their's the ruins of a small town, an enclave eyebot floats down the street, broadcasting patriotic tunes. Then you get to the school, which is your first introduction to the brutality of the raiders, again a marvelous piece of carefully thought out atmosphere.
Compare this to NV. You wake up to find Doc Mitchell smiling down on you. Then a character creation stage that takes all of 5 minutes as you walk around his house, not very interesting. He gives you a vault jumpsuit, which you really don't feel much attachment to, and you walk out the door. Your first view of the wastes is........ a small backwards town straight out of a Wild West movie. Victor the robot rolls down just ahead of you, and talking to him quickly gets old by your second character. Then you go out with Sunny Smiles and do a few errands shooting geckos. Ho Hum. Then, after more great tracts of words that gets tedious to go through, you get into your first quest. I'm sure you all know how it goes, but it means that it takes AGES before anything exciting happens.
And don't get me started on the Mojave Wasteland itself. It was a whole load of nothing. In FO3 you could start walking in any direction and eventually hit an interesting old ruin to loot. For me at least, a large part of the FO3 experience was simply exploring the wastes, because the Capital Wasteland was brimming with stuff while still managing to feel empty and desolate. But the Mojave Wasteland feels empty and desolate because it IS empty and desolate, which is the bad kind of empty and desolate. Exploring was not very rewarding and it was mostly there to create some space between the towns.
Part of this is becauseof the atmosphere, which has a number of elements I'll try to tie together here. First of all; ambient music, another area where FO3 excells. It was just right, and combined with the sound of the wind whistling through the dust, made the wasteland feel alive. Overall, Bethesda put a ton of time into creating the wasteland itself. It made simply running along with only the sound of my own steps for company something that I actually liked. If that got boring, than I'd simply turn on the radio.
FO3 had much better radio stations than NV. This is fact. Three Dog, though he felt a bit flat as a charcter when you actually met him, made really great broadcasts and had a fine selection of music. His NV equivalent, Mr New Vegas, cannot match up. I suppose this is because in Fallout 3 you were a really major player in the wastes, and listening to Three Dog talk about you in his broadcasts was one of the greatest things in FO3's ambience in my opinion. Mr NV,on the other hand, has bigger fish to fry than talking about one courier, so his broadcasts are a lot more impersonal. Not to mention that the choice of music Obsidian put into the radio stations REALLY gets old after a while, and has nowhere near the repeatability of FO3's tunes.
Now this is sounding like a huge NV bash, and it's true that I prefer FO3 to NV, but NV was great too. It had more features that I absolutely loved, such as disguises and mods. It had better voice acting, and a half way decent plot. Thhe character creation was also more flexible.
My point is that for the next Fallout game, my ideal set up would be to have Obsidian write the story, envision the locations, and handle everything relating to the lore and what features actually appear in the game. Then let Bethesda do their stuff and actually build the world, making slight modifications to Obsidian's ideas to improve their impact. And, of course, use Skyrim's engine. That is what I believe would lead to the perfect Fallout game.
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