I also think it is inevitable that the BOS will be in the next game if it is set on the east coast. I wouldn't mind it but they would have to get rid of the T-45d's and upgrade to repainted Enclave armor possibly. The Enclave needs to go away but i wouldn't mind seeing one more small base where the last enclave tell you how the enclave fell apart and maybe even have one of the soldiers as a companion.
I am sure the BoS will be in FO4 as well. I just hope that they don't play that big of role as they do in FO3. Hopefully we will run into other chapters sent East that still act like they do in the West. More references to the MWBoS woud be nice.
I don't think the Enclave armour in FO3 is more advanced. If you have in game info that says it is then I'll agree. Just without Damage threshold all PA was a Joke in FO3.