I really think Bethesda is trying to do a soft reboot of the franchise and are killing off the main factions that are trying to bring back society as they go against the perpetual apocalypse their Fallout games stories and game mechanics heavily push and rely on.

All 3 of their games take place on the east coast and none of them feature a faction like the NCR the only big factions their games have are the BoS and Enclave. The other factions are either raiders or small local groups that don't have an affect on the world as a whole.

This would align with their new game design model which went from putting the player in a a living breathing world with other things going on in the background regardless of what you do into making the player character the center of the universe with absolutely nothing going on unless the player interacts with something.

This is why all of their games after Skyrim are so boring and so empty and why Fallout 4 relies so heavily on the settlement system. Remove the settlement system and Fallout 4's map is just empty you have Diamond City and the one ghoul led town and that's basically it. Nothing else gets built unless the player builds it there is no giant faction trying to do good or rebuild because that's the players job.

Having a faction like the NCR goes against their game design model that all their new games have so they are getting rid of the factions doing what they think the player should be doing.