The NCR can be negotiated with. All of its endings more-or-less talk about how their people are sick of war and that they are finally going to end their campaign of aggression, at least for the time being. The Legion, on the other hand… There’s nothing stopping them from trying to attack you again. Mr. House seemed to be fine with that, as he wanted the Legion to stay a power in the East, but I don’t see how that helps Vegas.
Caesar is ill. If he dies on his own and you spare the Legate, that’s bad. If you kill the Legate, and Vulpes becomes the leader, that’s pretty bad as well. It seems like the best solution for Vegas is to wipe them all out and let the East fall. Sure, it’ll become chaotic and full of raiders, but they won’t be an organized threat to your new nation in the Mojave.
But Mr. House is always right. Arrogant and full of himself, to be sure, but his predictions have merit. Even going the Independence route, Yes Man follows all of his plans. So I’m not sure what to do to the Legion. Thoughts?