Mutations would have been minimal. In fact, had the Enclave isolated the FEV off the get go, there is no Master, and no Mutant army. Yes, we're aware there was no Master that early. But whose to say other monstrosities like the Deathclaws weren't running amok on the mainland at that time?
BoS would have been small. Enclave could have recruited people from Vaults, including Vault 15 which would have eliminated the Khans, Vipers, Jackals, and Shady Sands, thus the NCR. The BoS would have been the same size we saw in Fallout 1, as they accept no new members ( except in the rare case of the Vault Dweller ). The Enclave could have, but they wont. As you see in the opening cinematic for Fallout 2, they only gunned down the vault dwellers of Vault 13 and enslaved the rest. The Enclave just isn't the recruiting type.
Boom..Enclave nation.
I'm just saying if it "easy" to take the Citadel, it was just as easy to get off their butts and take over in 2082 when there was no opposition, and they had resources(Vaults) to leech from. That's a fair assumption unless they don't have any opposition from the BoS.
But, they didn't. Obviously for whatever reasons they didn't take over, and they didn't attack the Citadel. As LT pointed out, Enclave have been fairly ineptly written since conception. In fact, at least Beth was consistent with Enclave being fairly durp durp. This I'll agree with. The Enclave has been poorly written. They've made some stupid mistakes. I also still hold the thought that the Enclave could have annihilated the Citadel.