I don't agree. The Enclave showed no interest in vault City, and saw the V13 population suitable only for Experimentation.
But I hope this is the last we see of the Enclave as a traditional organised force.
The denizens of Vault City likely counted as mutants from the Enclave's strict viewpoint: they had lived in the wasteland for decades and required outside assistance just to reproduce. The events surrounding Vault 13 were partly due to chance: it had been opened before it was supposed to be, creating two groups from the same gene pool: one "mutated," and one "pure," an ideal group for their FEV experiments. The Enclave as it existed in Fallout 2 would have likely rounded up the people of any vaults that were still sealed or whose populations had not screwed up their biology the way the Vault 8 residents had, after they unleashed their plot. Furthermore, President Richardson said that they had been prepared for the war, he only cited the Oil Rig and the vaults specifically, but he could have had other places in mind too.
Having said this, I hope their presence is small to nonexistent in future Fallout games.