The main thing is the cities WORK. People survive, they're reasonably safe from the outside world. One city would never accept being ruled by the other, so the only way I could see them becoming united is by conquest, and why would the inhabitants of a city compromise their safety to go to war? The main reason for war is resources, so without any resources of any note in any part of the wasteland, what's the point of territorial expansion? Much more likely they'll accept their secure environments and not bother with something as trivial as a bit more land, hence the individual cities we see in Fallout 3.
But the original games were no different. The towns didn't unite yet were tied by trade routes, Shady Sands had the agricuture, the Hub had the water, Lost Hills had the tech, each had their own commodities that deemed them significant. In FO2 we saw an evolution in the form of communites attempting to expand to one another, Vault City, NCR and New Reno were fighting for Redding and it's associated ore resources. There was a spy in the NCR that was working along side John Bishop, the head of a family/gang in New Reno, who was trying to get a hold on Vault City in an unorthodox form of subjugation. And Vault City would have eliminated their ghoul neighbours if it wasn't for the Chosen One's intervention. In the end the NCR didn't so much wage any wars, it just expanded and annexed territory as it did. It was in Van Buren when we'd actually see the factions come to a head, and the story was to be based on uniting the factions. In this sense we saw a world that evolved through time, from survival, to progression, to full on humanity all over again.
D.C just sat there for 200 years it seems, nothing remotely similar, not just because "the core region did it" but because it's the basis of human survival and progression, towns wouldn't expand a little and say "that's it, I'm tired" their very existance shows the drive and determination to want to survive and succeed in this new world, and from there they would expand, not stagnate.