That's was done before FO3. FO3 says that the Enclave travelled East. Navarro could still be there and there could still be Enclave but after 38 years I am sure they would have A: Said to hell with it and went Merc or just looted everything and left. B: NCR finally made it to Navarro and took it. C: The BoS made it to Navarro and took it. D: The Shi might have even taken it. E: Enclave looted everything of Value and went East. Also Navarro was not that big and there would not be enough troops to stay behind to make the Enclave a worthy faction for New Vegas, plus Navarro is far way from New Vegas. Not all the troops at Navarro had PA.
If remnants of the Enclave remain, I find it likely that 40 years out from the events of FO2, most would have left for the east coast to take part in the disastrous plan of President Eden, especially those in a position of power or authority. Surely if the Enclave planned to usher in a new age by creating an area of pure humans in one part of the country, most of the organization would have been there or on route. Any Enclave members left behind to maintain the bases or foothold in the West would quickly fall into disarray with no purpose and no leader to give them a new one. They likely would have disbanded and gone their own ways, either to assimilate into the local population or become highly effective raiders with their advanced gear.
Even if the remaining Enclave in the West didn't disband, this shortly after FO3 (less than 4 years), they would be withdrawn and cautious, nursing their wounds and egos in private, and becoming largely unheard of until they can replenish their numbers. Considering they prefer pure humans, or at least as pure as they can get, they wouldn't be likely to recruit from the general populace, who they consider mutants, and would spend a generation or more rebuilding their numbers from children born to the group.
Regardless, we shouldn't hear anything from the Enclave as an organization in New Vegas, though it is likely we may run into ex-Enclave NPCs, newly disillusioned deserters from a failed cause.
Even if the remaining Enclave in the West didn't disband, this shortly after FO3 (less than 4 years), they would be withdrawn and cautious, nursing their wounds and egos in private, and becoming largely unheard of until they can replenish their numbers. Considering they prefer pure humans, or at least as pure as they can get, they wouldn't be likely to recruit from the general populace, who they consider mutants, and would spend a generation or more rebuilding their numbers from children born to the group.
Regardless, we shouldn't hear anything from the Enclave as an organization in New Vegas, though it is likely we may run into ex-Enclave NPCs, newly disillusioned deserters from a failed cause.
I Agree that the Enclave should not make a major (if any) appearance in FO:NV. What I am trying to argue is that The Enclave is not destroyed as a faction. They where beaten on the West Coast oil rig (And styles, from what I understand, Navarro holds the most advanced gear in the wastes. It has a whole bunch of soldiers, considering how many times you run into patrols trying to get to Navarro and the men actually in the base, and Vertibirds+Base defenses that could hold off almost any attack from the Brotherhood, Shi, or NCR. Otherwise what would have been holding these factions back before, considering they don't know about the oil rig.) And the Enclave moving east does not mean that the West coast Enclave would loose all their leadership. Col. Autum was probably just one of the "higher ups" the Enclave had at their disposal.
(also, the NCR and BOS would be somewhat weak at this point, They just fought a war against eachother where both sides had A LOT of losses. Moral and Men would be hard to come by for a attack on a group stronger than the BoS tech wise)
Another factor to take into regard is the fact that the Enclave could have had multiple bases. In FO2, if you are at the oil rig, on the same level as the president, the room right of the presidential office there is a map of the world. On that map there are 2 dots in California, 1 on the East Coast near DC, and many more scattered round the USA. I dont think they represent the Vaults, because there is only 1 on the East Coast near DC (while there are many vaults in FO3). If you where to look at them as Enclave bases, it would make out perfectly. 2 in Cali (Oil Rig and Navarro) and 1 on the East Coast (Raven Rock). It would not make much since either, having vault experiments on a map where you make you major strategic decisions. It would be more logical to have that information in a lab or observation terminal.
ANOTHER question to raise is: If they where sooo weak after FO2, how did they manage to create that mobile crawler + get hold of all those Vertibirds that we see flying out of RR after it is blown up? They either are not as weak as we think at Navarro or they had more bases scattered through the former nation. They even managed to create new and better Power Armor (meaning they have factories somewhere). Otherwise, it would be near impossible for them to get that equipment and manage a trek across the U.S.. It is even said that the Oil rig was only the HQ of the Enclave. That does not mean it is the only major base.
If, like you say, the MQ ending is only following the "good" trail, that would not eliminate the Enclave. Yes, it would weaken them, but they must surely still have more bases and soldiers elsewhere.
Cheers,
Mk II