I have a theory: the Enclave absorbed the Mid-Western Brotherhood of Steel as they headed East.
The logistics aren't particularly difficult. They would have potential access and maybe even the location of Vault 0. (For the sake of this theory, we are assuming the controller and thus the robots, were destroyed.) The Brotherhood may have manpower due to the local recruits, but the war with the machines took a heavy toll on their supplies and gear. Even at their strongest, Power Armour was very limited in number amongst their ranks, whereas it is the norm for the Enclave. The mwBoS had a few tanks that may not have survived the way; the Enclave had air superiority with vertibirds. It likely wouldn't even have been a long fight.
Or even a fight at all, if the Enclave had 'come in peace' in CW style. Power armour, soldiers, air support, supplies. The MW Brotherhood may even have accepted them with open arms.
There is no proof, of course, but there are signs that can be taken as hints.
1. We know the Enclave passed that way, and suddenly with Autumn, we have an Enclave faction that actually does want to control the wasteland, rather than kill all it's inhabitants. He genuinely, and has a faction within following him, does want to use Project Purity to win the wasteland, and hearts and minds, not wipe it out. Sound familiar? Almost as if some of the Enclave are no longer pure and indoctrinated. As if there is another tried and true method, that has worked before. The Enclave in Fallout 2 were not using this method.
2. Enclave numbers. The number of Enclave survivors, at least amongst their soldiers, has been raised as a plot hole after FO2. But, what if they had restocked on basic grunts, and officers? Perhaps the Mid-west had been their test case, and thus the attempt at winning the wasteland with propaganda. Maybe it worked before.
3. Shortly after the defeat of the Enclave in FO2, Lyons passed through the Mid-west... and found no trace/could not make contact with the Brotherhood spliter group. Perhaps they had taken such a beating they had retreated to Vault 0, and where not found. Perhaps they had integrated so well with the locals, they were no longer recognisable. Or... perhaps they had mostly gone East, retaining a base (Vault 0) and a few refuelling stations.
4. Chicago. The Mid-Western Brotherhood 'landed' and took Chicago, which was abandoned, first into heir campaign. And yet, supposedly it's got an Enclave base/outposts/refuelling station more recently. Interesting.
5. Advanced Power armour MK2. If you played Tactics, you could have been forgiven for thinking the Enclave were the Brotherhood at first glance. Even if you disregard it as coincidence, it adds to the theory. Taking the best of both armours, and coming up with what we see in FO3.
6. Controlled Deathclaws. We saw what happened when the Enclave tried to mess with Deathclaws before, in Fallout 2. It didn't end well. Yet... in Fallout 3 they have the means, via strange tech, to control them. In the mid-west, the beast masters could control the creatures of the wasteland. Perhaps through scientific study, the Enclave cracked the method? To be fair, this does not require the mwBoS, but still something that occurred to me.
7. Organisation. In FO2, despite the small fact they a re all dead, the 'government' behind the Enclave was very much civilian looking. Men in suits, secretaries, svckups. In FO3 the Enclave reminds me very much of the military command of the mwBoS, in almost every respect. Sure, this could be because it was mostly the military that survived and is the way of the military, but it shoudn't be dismissed out of hand when you consider the other points.
8. FEV and Eden. So, the FEV will wipe out all those not totally pure... almost a perfect way to get rid of tools that are no longer useful, now you have accomplished your goals. Like, say, over half your standing army that were recruited on the road, along with the rest of the barbarians?
There is more, but it's been a while since I considered it, and I don't have time to delve deeper. I just thought i'd post the theory, and see if I could spark some discussion.