I can actually de-irradiate water with a plastic bag and a bunch of sand. It's not that difficult to do with radiation or even any other substance. Distillation is a process which has been well known since forever. Megaton would be able to survive just by collecting water from the crater and purifying it (presuming the bomb wasn't leaking yet). As for the Brahmin, presumably they're descended from a single or multiple radiation resistant cows versus all being transformed by magic--even in the unrealistic way which radiation works.
That's presuming they could survive the immediate radiation caused by the bombs themselves, dust storms full of radioactive particles and radioactive rain (that old lady in Megaton actually tells us that they took shelter in the crater to avoid the dust storms). It would be possible, but it would require more than just a bunch of clueless civilians with seemingly no other resources than basic food and scraps to pull off. They would need some protective gear, people who knew how to use it, and some kind of organizational structure. But you would think that an organized group would know better than to come knocking at the door of a vault. Nuclear shelters operate on an amount of resources which can only sustain a certain amount of people, and stretching these resources to a vastly greater number would only lead to everyone ending up dead.
The issue with the animal mutations is that, besides dogs, every living organism in the capital wasteland seems to have mutated in order to survive. And even the dogs didn't look and act the same as your regular dog. How can a bunch of people with nothing but an open hole with a nuke in the middle of it to protect them avoid such a fate? It's mentioned that many took refuge in the subway tunnels, but since there's no trace of civilization left in those, it's safe to assume that everyone there needed to venture outside at one point or another.
It's also a missed opportunity, because the descendants of the humans left outside the vault being mutants (not necessarily ghouls, but something like the Slags from Fo2, or the swamp-folk from Point Lookout) whose interests are somehow at odds with those of your regular humans (the descendants of vault dwellers) would make the Lone Wanderer siding with Enclave a lot more likely and believable. It would also make the Enclave more than just a cartoonishly evil reference to Fo2.
Point Lookout is OCCUPIED, though, which is the traditional reason why people can't just move to a new location. Specifically, it's occupied by a bunch of super-mutant tough local mutants. It's possible the Capital Wasteland has a bunch of people who don't want any newcomers.
As for Raiders, there's a good theory the Raiders of the CW may have wiped out other settlements we haven't seen and/or be the descendants of the Vaults which warped them into bloodthirsty lunatics.
Point Lookout is occupied, but the locals are really only hostile towards the player to give you something to shoot at (and they still won't attack you if you just keep your distance). They coexist rather peacefully with all the non-mutated inhabitants of the swamp. And whenever a similar scenario happened in history, of a region's inhabitants facing annihilation due to environmental changes, the said inhabitants moved or died. You might argue that the people of the CW simply aren't dead
yet, but it has been two hundred years in a very, very hostile environment. If the regions they intended to move to were occupied, they would probably have no issue displacing the natives. It's a simple "us-or-them" scenario.
The issue with raiders isn't really why they are such bloodthirsty savages, it's how they're even there. The raider, like any parasitic organism, needs a host. Even if we presume that most of the raiding in Fo3 actually occurs between the raider gangs themselves, it still requires resources coming into the their circle of raiding from outside. And for that outside source to even remain in existence, and thus keep the raiders alive too, it needs to produce enough goods that they are able to survive and maintain this production level despite losing vast resources to the raiders.
Or we might assume that all the raiding is just a sadistic pastime, and that their main source of food is actually the local wildlife (and what does this wildlife even eat - beside each other?), in which case the question of why they are such bloodthirsty savages is the deal-breaker, as a hunter-gatherer lifestyle would cause fierce competition amongst different gangs of raiders over various hunting grounds and cause constant friction, with the advantage going to those who didn't waste resources on pointless sadistic excursions.
