I was thinking a bit earlier about the Enclave numbers presented in FO3, compared to the end of FO2, and I think I may have come up with a plausible explanation to address the drastic rise in the Enclave population between the two games, that involves only In Game Cannon.
In order to understand where I am coming from, there needs to be a basic understanding of two groups in the FO universe: The Enclave and the Vaults. As we all know, The Enclave hates all non-humans, and would never recruit from the wasteland. This is why it is hard to explain the number of soldiers the Enclave had in FO3: Pure blooded humans do not appear to be common in the wasteland and most of the Enclave died on the Oil Rig. But there is another group of pure humans that we all know of: The Vaults.
The Vault dwellers in every game have shared a distrust and hate for all outsiders; close-humans, Mutants, and ghouls. FO1 showed that Vault 13 distrusted the outside world (and thought it to be overrun by the master's army), Fallout 2's "Vault City" showed the vault dwellers using the wastelanders as slaves. And FO3 showed Vault 101 was unwilling to let its general population to move outside.
This is where my idea comes into play. What if the Enclave recruited from the Vaults? As we know from FO2, the Enclave knew the vaults locations. They also knew the passcodes to get into the vaults (as seen in FO3's quest "trouble on the Home Front"). The Vaults, being the only bastions of pure human left in the world, would be the only place for the Enclave group traveling East to replenish their population count. This would also be plausible because the two groups shared a common mistrust of the outside world and wastelanders (and both still believed in America, as we can see in the V13 posters during FO2's intro, and Vault 101's flags throughout the vault). This idea would also explain the transmission from the Enclave in the overseer's computer during "Trouble on the Home Front" quest in FO3, that I mentioned earlier, where the Enclave was trying to get access to Vault 101. (correct me if I am wrong, but didn't the Enclave say that they would take them somewhere safe in the transmission they sent them?).
The only reason I could see someone disagreeing, is because they murdered the Vault Dwellers in FO2's intro. But that would only be because they didn't need the manpower then and only wanted to test the inoculation/FEV. With the Oil Rig gone, they would be more than happy to take in more pure humans. It would be the only way for them to survive.
Also, this idea would only apply to unopened vaults. Vault City would have been exposed to the FEV and the people unusable. Vault 13 and Vault 101 type vaults would be the type that would be looked for.
So, if this idea does prove to hold merit, it would explain 2-3 things: Enclave Numbers in FO3, Why the Enclave seemed to travel towards Chicago between FO2 and 3, and why the Devs seem to be lining them up in a future game (Chicago and ED-E).
Cheers,
Mk II