Does wiping Megaton off the map even DO anything, really, OP? Megaton is not important. Rivet City is not important. They're a collection of shops, and some player housing. But the story does not *NEED* them. It stings if you want it to, but the only real player in game who talks about it is Dad Qui Gon who chides you like you just stole something, not just killed a dozen people and wiped off a 60 year old town.
Part of this is, well, Bethesda didn't care. A town to them is just something to show off a zany post-apoc trope than a real post-post apoc society.
Megaton is made of junk around a fucking functional Atomic bomb. Even just ripping it apart should had been the first train of thought to any settler here, because the Church of Atom came AFTER Megaton was made, not before, right?
You have a town on a bridge, that was neat but besides the vampire quest was never revisted. Related to that are the vampires in the tunnels. Because yes, this is a game that needs fucking Vampires??
Rivet City, instead of being this ex-military ex-government hub on an aircraft carrier...is just a bunch of idiots with some scientists on an aircraft carrier.
Tenpenny Towers is, somehow, a bunch of rich fucks in the most blasted out wasteland, far away from fucking anything, acting snobby. That's something I would expect more at that playboy palace in the city than out in bumfuck nowhere.
Then you have the kid's town, because yes - the wasteland sends all their kids, across the fucking map, into Mutant territory, to be raised without oversight or protection. Then they throw you out when you're big to another small hamlet in bumfuck nowhere again under Mutant influence, and is dulfully picked the fuck off by the Mutants.
The slavers, raiders, and mercs make the most sense, because they're slavers, raiders, and mercs.
Don't forget the drama of the guy trying to fuck the stupid girl, the only two people in a town out in bumfuck nowhere, when they could had easily shoved that into Megaton.
Then there's the trader settlement. Nothing to say here, that's fine. They could had done a lot more with it, but eh. Trade hubs are expected. The Mechanicst and Ant-woman were a fun aside.
Obligatory Ghoul Town.
Oh and the Republic of Dave. It's...alright, I expect bullshit petty tinpot dictators to arise out in the waste. Am I forgetting any? The dead rock town we never got to see? The town with the ants? Oh, the cannibal town, right. Uhh..Cannibals, dressing up like its the 50s and everything is fine. I basically just shove them up under Raiders, kill them. I wish I could send Rivet City or Megaton or BoS by to take the kids in..... Or even send them to Little Bigfoot, but nooO!