Honestly with the Brotherhood I would have loved it if we could spark a rebellion within the chapter. Perhaps bump into a group of the troops who deserted after they saw that the BOS was heading down their crusader path after both Lyons died. With that we could see them go back to simply protecting the people and not bullying people for their energy weapons or power armor. As well as to give up this genocidal tendency with any "abominations". Hell back when Lyons was in power they pretty much gave Fawkes amnesty and he was a god damn mutant. With that said we can see their major force leaving the Commonwealth after having taken out the big threats to the people as well as taking out any experimental weaponry that can wipe out large amounts of people. After which they can leave a small force at Fort Strong to ensure that things run smoothly as the people kick start the CPG once again.
