I actually have an interesting opinion of what could have happened to the Enclave that if I were making Fallout 5 I'd implement. Mind you its a work in progress.
In their exodus to the East Coast the Enclave split up into two groups. The main one took most of the troops and equipment and was lead by Colonel Autumn to the Capital Wasteland to set up the Enclave 2.0. A second group was dispatched to the Southern United States (the setting of my Fo5) to activate Phoenix Project bunkers (Yes I know I ripped off Deadlands: Hell on Earth shut up!). Basically the US government got in on the Vault act and got Vault-Tec to design them bunkers filled to the brim with weapons and equipment for the cryo-frozen US military project volunteers (basically those the tests say would be the most likely to go along with whatever the government decided to do in the event of a total nuclear war). The plan was to activate these bunkers full of recruits to help rebuild the Enclave back in the Capital Wasteland. They were halfway through the activation process when Raven Rock blew up and they only made it back to the Wasteland in time for the events of Broken Steel to conclude. So they go back to the South and carve themselves an area to rule reactivating every bunker they can find to refill their armies and try to carve themselves out a New America.
There's more to it than that that really turns the Enclave more into a gray faction (governing an area instead of being shut up in some Enclave base lessens their extremism a little though they are still hated by Super Mutants and Ghouls), and other details that really flesh out the story but I've decided that this is the most I'll put out for now unless anybody wants to hear more.