I've given this a bit of thought, and I think I've found a cool way to put multiplayer into Fallout 4. I could never actually do it myself, but regardless, I think it would work.
So what I was thinking is that one Team would consist of 3 players in power armor with some BOS Paladins to assist them. They would be know as the 'Assault Team.' Their goal would be to take the Institute Fortification, or bunker.
The Opposing team would be 3 Institute Soldiers, with synth support, defending said location from the 'assault team.'
Maybe, in order for the BOS team to win they would have to capture certain points and locations along the way.
Maybe even adding artillery support into the mix, along with some other extra's, like being able to call in a paladin on a vertibird for help. The Synths could use a stealth ability to turn invisible as their 'support.'
If you have anything to add, please do so.