In terms of atmosphere and setting, I liked both, even though they were different. It doesn't have to be either/or to me. I actually LIKED that they were different, because it gives a sense of verisimilitude in that different areas would have developed differently 200 years after the bombs dropped.
Washington, DC was more heavily bombarded and had things like the Super Mutant vault influence its slower post-apocalyptic evolution. It also had fewer truly functional Vaults out of which people might resettle the land--all of the Vaults in the area that I can recall were largely some of the more whacky experiments, where fewer people survived to get outside; the only normal-ish Vault with its work ethic experiment was 101 which had its isolationist overseer that prevented them from settling the outside world. That meant most of the human inhabitants were descendants of outside-vault survivors whose society would probably have devolved far more during the direct post-war before re-establishing something more resembling civilization. I do wish that Bethesda's designers would have put a little more thought into the world development--the Washington area is effectively swampland and without human maintenance would largely have devolved back into a swamp, and along with that there would have been a lot more vegetation, however mutated (but 200 years after nukes is enough for plants to grow back--the area around Chernobyl is largely green now after all). And of course the whole water purification thing was silly; the Potomac's a pretty damn big river with tributaries in areas that would have been far less affected by the war, and in 200 years much of the sunken Fallout should have washed out to the ocean. But I think they still established an interesting atmosphere.
Las Vegas was minimally attacked--there was less concentration of attacks and many of the ones that hit were deflected by Mr. House's defense system--so there was more to rebuild from. And there were a couple more "survivor" vaults--27 put out fine survivors, however gambling obsessed. I get the sense 3 got some people out before the Fiends took over--they were actively trading with the area before they were attacked. And the armory one whose number I can't remember obviously at least the people who became the Boomers survived. So there were more people, more records of past civilization, and more tools with which to rebuild. Oh, and there are the Followers of the Apocalypse, whose purpose is to help recover past useful tech to rebuild society--they haven't made it out East yet, and that also may have some influence.
So the evolution of each area, side by side (so to speak) makes sense, and to me the differences are part of what makes the Fallout setting as a whole cool. I like the post-post-apocalypse world of New Vegas and the more struggling world of the Capital Wasteland equally. I enjoy the atmosphere in both, they are realized well and feel like complete worlds.
My only thing where I personally prefer New Vegas over Fallout 3 is I like the main plotline better. I felt like in New Vegas I had some real choices to make and I felt like the struggle between the warring factions was central to the Fallout series' theme. In F3's main plot, I felt like a spectator rather than the protagonist, and frankly? My douchebag, deadbeat Dad and his water purifier can suck it. The fact that I didn't have the option to kill him myself (nor even get any dialogue options to express I was glad of his demise) is particularly sadmaking.
OTOH, I liked many of F3's sidequests better.
Oh, and New Vegas definitely wins for having better companions. (Veronica, how do I love thee? Let me count the punches. One, two, three...)
But both games had some great areas to explore (on replaying New Vegas, I found the sewers which I'd never found or done anything at all in my first game; in F3 I've often found some random little cave or shack I hadn't noticed before), cool atmosphere, some neat boss fights, interesting factions. I think both are worthy entries in the Fallout series and I feel sad when people act like if you like one, you must hate the other -- there's plenty of room for both for each of their strengths to shine.
