If the Barnaky Ending is the canon ending then Enclave definitely have aplace alongside the MWBoS
I really hope the http://www.youtube.com/watch?v=u2ZcpcO7C58 is canon. The story would be awesome. The Enclave in Chicago would be alot like the MWBoS that have started to form a fascist military dictatorship that goes from Chicago to Colorado but the Enclave would have had to change as well. Dispite the BoS acting alot like them they are still impure in the eyes of the Enclave but if the Enclave in the area were smart they could become allies with the bos.
Way I see it. The MWBoS fight a bloody war against the Super Mutants and then the Calculator. They force settlements to aid them by giving food, ammo and their best and brightest. Many people do join willingly but the BoS treat them as cannon fodder. The Elders let mutations join because they can be very useful in places humans can't due to radiation.
Vault Zero falls to the BoS and Barnaky becomes one with the Calculator. The BoS are happy to have General Barnaky back. There is a push to make him the head Elder of the MWBoS. The famed warrior (you) who is also a General backs the move to make Barnaky the new head elder. Which he does become.
He soon recalls all mutations from the BoS armies and orders them back to their home bases were they are disarmed and tagged, later to be sent to work camps. BoS stops letting mutations join. Laws are pased and any mutation within the BoS' territory is to be rounded up and also sent to camps. (work/death camps) Which is the start of the great betrayal.
Elders that were most against Barnaky becoming head elder are removed from power. Soon purges happen with in the BoS, anyone that was against barnaky or seen to aid mutations are also sent to the camps. Entire settlement get put to the flame. Soon the Mutant Liberation army forms. BoS caravans and outpost get hit. Work camps are liberated. The BoS see a dramatic fall in people willing to join the BoS. They start having desertions.
Human numbers are replaced more an more by calculator robots and more purges follow fearing an inside job. The BoS stop trying to contact the West in order to get their own house in order.
Biggest blow happens when rouge BoS members set off several bombs within Vault Zero in a failed coup d'état. Many of the calculators systems are damged beyond repair. Barnaky lives but finds has less control over the robotic forces. He can't control them all at once and the ability to make more robots is severely hampered.
Mutant Liberation Army makes allies with whats left of the reaver movement and are supplied with EMP weapons. The remaining slaver/raider groups once again become stronge and prey on BoS settlements and outposts.
Decades of bloody Guerrilla warfare against the MLA and the predation of other factions (slavers, raiders) have driven the MWBoS back to their remaining strongholds such as Vault Zero and Cities in between Colorado and Chicago.
Lyons and his BoS are sent out to make contact but don't really know where they are, they know the MWBoS went East. They took a path that takes them away from the MWBoS strongholds at Vault Zero and the others in the Midwest. As Lyons gets closer to DC he hears rumors of people that have similar tech and a simbol are in the area. Lyon spends along time hunting down those rumors. MWBoS fearing that Lyons is just the tip of a larger army coming up from the south east, do what they can to not be found by them.
Lyons is persistent and soon the MWBoS send out a group of their own elders to make contact. They tell Lyons that MWBoS are just a few hundred men and women close to Chicago. Lyons having made contact goes on to the more imprtaint mission of heading to DC.
Like the Barnaky ending states its a war the Mutant Liberation Army is distended to lose. MWBoS have seen bitter defeat after bitter defeat for generations and are now a shadow of their glory days but time is on their side. Mutations can't reproduce and the ones that don't fall to the BoS will be taken care of by father time. The humans and fellow bos memebers that sided with the MLA grow tired of fighting. Seeing as how they have crippled the MWBoS and liberated much of their territory. They just want to settle and farm, the threat is all but gone (so they think). After generations of war the younger generations don't take up the fight.
Maybe the MWBoS will find an ally in Augustus Autumn and his advanced tech can help the MWBoS take back what they lost.