Yeah for the  game endings, I think some modified versions of the endings need to be decided upon. For instance, Fallout 4, if the Minutemen destroy both The Institute and Brotherhood, that knocks out a couple factions for people to potentially RP as. 

That's not to say The Minutemen can't win out, but instead of wiping them out. Perhaps The Institute is evacuated successfully and The Brotherhood retreats after Liberty Prime is destroyed (just an example). 


Edit: I'll just say too that if the ending can be modified a bit. I'd like to claim those Institute remnants as a potential faction.