I'd like for the Midwestern BoS to be made canon to some degree, since on territory alone they're possibly the biggest nation on Earth and, based on testimonies in Fallout 3, they have splintered off from the BoS and are most likely resentful. The Western BoS is weakened and fading, doomed to either disappear or be assimilated into the NCR, whilst the Eastern BoS, for all their bravado and zealous loyalty, aren't really a match for such a powerful force. A fascist-militaristic nation like that with a (potential) access to a vault that manufactures mechanical troops would be a dangerous and immediate threat to every faction in the Wasteland; if it were explored in terms of what it provides to its people as well, it could become a rather balanced and interesting faction to star in a possible Fallout game.
As for the actual topic of the thread, the Chicago Enclave are most likely either gone or lack any real presence. The city itself has a strong Brotherhood presence nearby and, assuming they didn't colonize it already, is completely deserted and blanketed in storms year-round. Though the isolationism would weaken it, I'm not sure to what degree it would do so, as Wheatley mentions several outposts in Chicago, not just one.
A few would probably be abandoned for a variety of reasons, and the remaining would either grow more isolated and weaker or strengthen their bonds, depending on how they take the news of their defeats at both Navarro and DC. If the Midwestern BoS is to be considered canon, they'd probably be raided or assimilated, as this particular branch of the BoS hasn't come in contact with the Enclave in any way, shape or form before; the former seems more likely though, as the Enclave would respond with hostility.
If the Midwestern BoS is not to be considered canon, then the Enclave would have little to fear from the surrounding tribes (assuming any would dare venture into the ruins of the city anyway) and would probably establish some sort of underground presence, like a secretive version of the Institute, but far less well-equipped.
Honestly, I don't know what they would do with themselves at that stage; perhaps their military branch would take over and, in their struggle for survival, they'd become like a new BoS in terms of hierarchy, but bent on the purging of Wastelanders rather than protecting them from themselves and they would capture technology for their own benefit, without a pretence of greater good.
Or perhaps their military will dwindle away, as less capable soldiers are born and more are killed by the hostilities of their environment, and they would become a primarily scientific group, paranoid and suspicious of outsiders, forever fearful that they will one day be massacred like Navarro and Raven Rock. They might even rename themselves to hide their origins.
