I know I said that the Enclave, as a major antagonist, in future games would seem implausible. But, that doesn't mean it won't happen. It wouldn't surprise me a bit to see a future game with a still powerful Enclave, using Deathclaw stormtroopers, based on the moon, conspiring with ALIENS, launching HUGE SPACESHIP ARMADAS AT EARTH..............to conquer primitive tribals.
However, on a smaller, local scale they could make for some interesting encounters. You could have a group of Enclave people in denial about the Enclave's fortunes still trying to hang onto their identity. They might still have some story potential. But, they should not be utilized again as a major force.