Lyons probably controlled all contact channels with the West Coast Elders. By the time FO3 takes place, the Outcasts are trying to establish contact with the West Coast, but are not succesful.
That is true. But it couldn't take them much more time after Fallout 3 for them to establish contact, it would be interested to see the West Coast step up in the region on the side of the Outcasts in an attempt to 'break the back' of a rebelling Lyons.
Why would they need to scratch the original canon? They relocated the game to the other side of the country, and both the Master and the Enclave in FO2 were, at least during the time the games took place, pretty much local villains, not ones that spanned the whole of the United States. They could have easily created new factions of comparable strength on the East Coast if they wanted. In fact, the Institute (Commonwealth is the area, Institute is the faction) would make a better FO3 villain than the rehashed Enclave. Maybe they would replace your Dad (and some other key people in the wasteland) with an android copy in the middle of the game, without your knowledge, to gain a foothold in the Capital Wasteland with their obedient human-looking spies?
Androids are a very scary concept, anyone could be the enemy preprogrammed to kill you once it gains your trust and the trust of those around you, in fact, that sounds quite familiar. Oh, yes, isn't that the entire plotline behind Battlestar Galactica, I guess, if it worked to make that show cool and popular, why not now?
The Enclave, however, does span the entire country.
Anyways, I do agree, the Institute interested me more in it being the Commonwealth of New England, that is what it would be called wouldn't it? It would be poetic justice for Massachusetts to finally be the bad guy and not always saving the day like it has historically. The backwards 'Railroad' was entertaining.