Sheffield mans my bar in town ;p Brew bot usually hangs out next to the stand.
MM lore is easy in future games. "People of Commonwealth banded together and told everyone to GTFO and dealt the Institute and BoS a crippling blow, although neither were totally destroyed. Commonwealth was merely a setback!".
Basically it lets them do a power reset on the 2 overpowered factions techwise so they can keep the series rolling. NCR is powerful, but they lack the tech. BoS and Institute, if they put their minds and muscle to it, were the only 2 surviving factions that could legitimately rule the world.
Institute: They literally are the only ones with future tech that developed well beyond the confines of pre-war. They aren't interested in conquest, but they are interested in reclaiming the surface eventually. They run the risk of repeating the mistakes of the past, though, in terms of science without morality (ie, Vault-Tec). They don't care much for the surface folks unless they can be useful (ie, Institute grabbing the best scientific minds from the surface and letting them go to town research wise once they are initiated).
BoS: Huge military machine now with the most advanced pre-war tech available, such as Liberty Prime and a flying aircraft carrier. They are interested in conquest of all tech, which ensures only they have the toys. They don't care about "civilians" unless they can provide them with supplies or show promise as BoS members (scribes or soldiers).
The direction the BoS is headed in wouldn't result in a rebuild for the world and basically it would just be the status quo. At least with the Institute, you could argue that some of their advancements would ultimately benefit the planet. For instance, the Warwick seed experiments are plants that literally remove radiation from the environment AND they are super nutritious. And the FEV research, while morally questionable in terms of how they went about obtaining subjects, did potentially have the chance to reverse the mutations that created Super Mutants and other mutations. I mean, the Enclave just wanted to kill them all (mutants), at least the Institute was seeking an actual cure for FEV.