Well, those supermutants were under orders by smarter beings to invade. They weren't just doing it. Also, the supermutants in Fallout 3 are mentally retarded. I don't mean as a concept, I mean the supermutants themselves are presented as being retarded. Even though supermutants are long lived, tough, radiation resistant, and strong, they're still fucking retarded. The idea that they didn't Darwin themselves out of existence in the two centuries since the bombs dropped is very questionable. These supermutants are running around with missile launchers and frag grenades in the game.Which only reinforces the idea that having super mutants on your doorstep is not good for a budding civilisation
Their only means of perpetuating their species is catching humans and dipping them, a la Fallout. Which makes you wonder how they even figured that out considering The Master didn't even realize that supermutants were sterile. Also, how did they maintain their FEV stock? People never figured out how to deal with the supermutants in 200 years with streets littered with rusty mini nuclear bombs?
The main problem with all this, other than there shouldn't be FEV on the East Coast, is the 200 year thing. markec makes a good point about people leaving if the supermutants were that bad. It's not like they have much there to begin with, even after 200 years judging by the game world.