Perhaps density isn't the correct word. FO3 felt artificial. There was a fair amount of stuff in a tight area in New Vegas - but Vegas gave a good reason for that density. The people you ran into were there because of Vegas and Hoover Dam.
I can see what you're saying, and I suppose if placed under a careful lens, not everything in these games makes logical sense from a real life perspective.
By comparison, FO3 had small pockets of people - many of whom lacked to have a way to grow food, or access fresh water, or really to have any reason to stay there. There are still ruins that aren't lived in, nor have they been cleared out. Open vaults filled with relics which no one has touched in 200 years.
There weren't that many places in FO3. The major civilization centers were Megaton, Rivet City, Tenpenny Tower, and the Underworld; and calling some of them major is stretching things a bit.
It also seems like there wasn't much of a crop industry and that people mostly farmed Brahmin, which I suppose grazed on any small plant matter. Tenpenny and the people who occupy his apartments are supposedly rich enough that they can import what they need. There are also a few interesting cases, such as the kids in Little Lamplight eating cave fungus that is revealed to grow best when it has dead people to fertilize it, and then there's the small settlement populated by cannibals.
The entire game world was designed around giving players things to do - with no thought at all to internal consistency or believability. Wandering around a post-apocalyptic theme park, versus a world. None of the previous titles had felt that way - places had a reason to exist outside of the player.
There are definitely instances (e.g. putting Harold in the game) of what you're describing, but I wouldn't say it stands as a central point. I don't know what their intent for the game was, but to me it played out in a way to suggest that it was exploring the precursor events to civilization being able to bootstrap things to the point that they can rebuild at a reasonable rate. Prior to the end of the original game, it seems as though the capitol wasteland was too much of a hellhole to support a large population and the trappings of civilization that come with it.
So I think that they may have had an interesting idea, and after they fleshed that out, they just added a lot of things to do that weren't really tied to anything. I think that they also felt as though they had to add a lot of things (e.g. the Brotherhood of Steel) to the game as a nod to the fans. In bringing a new entry to a series that hadn't had a main entry in about a decade, there was probably a lot of pressure to include elements from the previous games, even if they didn't make a whole lot of sense.
Had they gone all the way on that route, I might've been more into it. They didn't really do too much with that though. For all the talk of the importance of water, you'd have 1 beggar outside of every town who seemed to actually be inconvenienced by thirst. Nobody else seemed to mind that much. They just hung out in their little walled, farmless, waterless cities without a care in the world. Waiting for a player to show up to send on some errand or another.
Once again, I have to disagree with some of what you're saying. If you accept that the land is mostly useless for farming and possibly only good for grazing, it's not too hard to realize why people mostly stuck to their towns. Megaton had a water system, so it's reasonable to think that they had a water supply that wasn't completely irradiated. Rivet city, the only other large settlement, had scientists who would later go on to solve the irradiated water problem, so it's not unreasonable to assume that they could solve the problem on a smaller scale, at least enough to keep the settlement going. That they had beggars outside the cities was most likely just to reinforce the notion that good water was scarce.
The land outside of these settlements hadn't been tamed either. It was overrun by wild animals, bandits, and a lot of super mutants. Given that, I really can't blame the average person for not wanting to step outside of what relative (even the settlements weren't all that safe; for example, Big Town seemed to be on the brink of getting wiped out) safety they could find.
Everything would have gone over better if it were a little more well written, but like I said earlier, there was probably a lot of pressure to include elements from previous games that wouldn't necessarily make a lot of sense. If the next game is set in Boston, I'm really interested in seeing what Bethesda does with it. In FO3, they introduced the Commonwealth, which was only really touched on in a single quest, but is implied to be a much more civilized area. It's also something that they developed themselves, so it will be interesting to see what they can do if they don't feel constrained.