Brivoo
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I'm just pointing out that civilisations like Caesar's Legion have, depressingly, worked over and over again. Diseases like cholera and dysentery have ultimately had very little impact on some of the biggest empires in the world. I'm not saying Caesar's Legion is the best option for the Mojave, but it is a viable one.
Civilizations like Caesar's have worked in their own time period. They weren't necessarily at the technological forefront of their era (though a lot of them were), but they were always innovators in one way or another.
Caesar is a tactical and strategic genius; if left alone, almost all Legion operations go according to his plans and the simple fact that he's managed to become a considerable and even terrifying threat to both the NCR and House (both of which are considerably better equipped than he) speaks volumes about his cunning. If he had been a military leader and nothing else, like the Legion's General, but unfortunately he isn't. He's the leader of an entire civilization, and the moment it stops sustaining itself on conquest it will perish unless he learns to adapt and use technology.
Though true that a lot of folks commend the Legion for the safety of its roads, I'd take it with a grain of salt. His entire nation is focused on the war effort as of New Vegas and has been for its entire existence; dissent is unlikely to develop when absolutely everyone is involved in the process.
As for the actual topic, I don't think the Enclave should come back as an actual major faction, but remnants of some sort would be fun, not entirely dissimilar to the Yangtze memorial group. Say you find a group of scientists hiding out in an isolated area, trying to survive and extremely paranoid of outsiders; as you explore, one of them asks you to go look for his grandfather's corpse and retrieve a sentimental item in a dangerous area. You arrive to find a vertibird wreck from what looks like ages ago; you retrieve the locket and take it back to the man, who thanks you and explains that his grandfather died fleeing from persecution like a lot of his faction's people.
Keep it vague but implied, essentially.