In Fallout 2, Frank Horrigan said "You've done nothing here. The work will go on." as he activated the self-destruct on the Oil Rig.
While it is indeed true that in Fallout 2 more Enclave installations on the US mainland were mentioned, those apparently weren't full colonies, rather research outposts, communication and observation bases and the so called 'hot spots' where some Enclave personnel took shelter before the War.
I don't know where it was mentioned but the Enclave took the second (or first) GECK from Vault 13 with them when they rounded up the Vault 13 Dwellers as they needed it to establish a colony (which by its own is weird, why would the Enclave not have a number of GECKs or better equipment on their HQ?)
There was nothing to the number of troops and technical personnel that the player found that worked at Raven Rock, that managed to survive the destruction of the Enclave at the West Coast.
The only better explanation would have been that this personnel had been stationed at Raven Rock from the start of the War and that these are their descendants, raised as Enclave personnel and soldiers, never having known Richardson and his cronies other than through radio messages.
Of course the idea would still suck, why bring the Enclave back as the main enemy, or Super Mutant forces.
Come up with a new enemy like Van Buren came up with disgruntled NCR soldiers, various raider groups, two cults of slavers, and ODYSSEUS' robots.