Add [more] exposition clearly stating that the Enclave only existed at the rig, and the new Navarro base, where they were only just getting a toe-hold on the mainland.
I also wish it had been made more clear in Fallout 2 that the Enclave presence on the mainland was limited and that they did not have an army in the thousands but in Fallout 2 itself I think it is mentioned a couple of times that the Enclave has a couple more outposts in the wasteland outside Navarro.
But I don't think these have the number of personnel that could possibly show up in Bethesda's Fallout 3.
For the rest a couple of suggestions for retcons I would suggest (or would have suggested if I remembered them) have already been posted here.