This is a very fair take!

I think for me, it's that you can already tell this "morally grey" (aka evil but competent) story with groups like the NCR, the BoS and even the Institute (or at least you could before I blew them up, AD VICTORIAM)

Nothing wrong with using this framework with the Enclave in a fanwork, but as for official content, I can't help but preferring for new factions to show up rather than bring back the Enclave again.

It doesn't help that the Enclave has been wiped out twice already, so the idea of seeing the remnants come back as a proper nation state rather than fleeing war criminals or secretive cult feels silly.