Remnants. They are nothing but remnants. No one is denying that there is remnants.
The problem with your thinking is that you think remnants could and will equal thousands upon thousands of Enclave that control the whole Eastern half of the United States or the Midwestern United States and that isn't the case.
All the Enclave in Fallout 3 came from Navarro. Navarro was the only manned base the Enclave built on the mainland United States and it was built for a reason and out of what could be called desperation. The Enclave were happy on the Rig. The Rig was safe from contamination, from mutation. But the Enclave discovered that the mainland, the West Coast of the United States had armies of Super Mutants and other mutants (including humans) were increasing to unsafe numbers. "They might discover the Rig" type responce happened.
So the Enclave created Navarro. They went to Mariposa, Vault 13, Arroyo and New Reno to get what they needed to create the Curling Virus and Vaccine. The Rig was destroyed killing all the leadership and the bulk of the Enclave. The only Enclave that survived were those at Navarro and Navarro wasn't even fully staffed at the time.
So that means the Enclave in Fallout 3 were remnants to start with. They would have been the ones to establish the Outpost(s) in Chicago. The Group that headed East were only apart of the group that was at Navarro. The others that stayed at Navarro were either killed in the battle with NCR or gave up like the Remnants in New Vegas had and tried to start new lives, only to be hunted by the NCR and Brotherhood of Steel.
The scattered little groups throught the DC area are also Outposts and they only had a couple of people at best. If you don't count respawning for game play purposes, there aren't that many Enclave in Fallout 3 and Broken Steel.
Lyons and his people said they would hunt down any that survived.
So a group of people if they still hold on to "we are the only pure blood humans" will not mix with outsiders to rise again.
Also Helfire Armour and all that was built at Raven Rock/AAFB also destroyed.
The only place the Enclave existed other than the Rig was Navarro. Navarro was an under manned outpost. All Enclave we see in Fallout 3 came from Navarro. There aren't large numbers of them out there with a huge base and all that. Raven Rock was their last hope and it was destroyed. AAFB was destroyed. As an organized faction with any real power or threat, they are all but dead. If they remain as organized group at all.