* The Super Mutants are created by FEV exposure to a Vault - totally unrelated to the Master.
* The Brotherhood of Steel sent a small army under Lyons to cross the country and take up residence at the Pentagon.
* The Enclave fled from the west coast because they had their ass kicked THAT thoroughly.
and no one really noticed anyone else until later. It's a hell of a coincidence but it's not like they just snapped their fingers and said, "They're everywhere!"
True, but was there really any need for including some of this stuff? For example the Super Mutants served absolutely no purpose in Fallout 3, they weren't really tied to the storyline (raiders or other mutations could have easily taken their place in the Brotherhood's back story) and didn't have any quests attached to them. They were a filler enemy that was inserted into the game simply because Super Mutants were the primary antagonist of Fallout 1. While I'm not as bothered by the presence of Super Mutants in the Capital Wasteland as some people, I think that their inclusion could have been handled much better.
I agree to an extent. The Talon Company mercs were just a filler enemy, their purpose for being in DC was poorly realized. The Institute on the other hand has potential I think. Yeah at the moment it's little more than a blatant rip off of Blade Runner, but it has the potential to be so much more than that.
If you just want to do a game about Post-Apocalypse RPGing, just call it Wasteland 2 or "After the End: the Shooter."
Agreed, I felt that Bethesda did a fairly good job at connecting Fallout 3 to the past games and their lore despite being set on the opposite side of the country. I really do wish that the Enclave hadn't been reused as the primary antagonist, though.