I hope we see very little if any of the enclave or BoS going forward, and I think with the enclave we have a good chance of that, but I bet Bethesda makes the BoS a main element in every game... they made that armor image the icon for the game, and honestly I don't think they could stop themselves from pimping it out more and more.
I would love to be surprised though.
As id software has been acquired by ZeniMax and has done a lot of development for http://bethblog.com/index.php/2009/07/13/rage-cover-story-in-game-informer-teaser-site-live/, I wouldn't be surprised if the course of the future Fallout would change drastically, as Rage and Fallout worlds aren't too far from each other, artwork if not already restricted to the EA deal allows improvement for both games, and id devs could influence Bethesda, although it's probably more working in the other direction. At least I think ideas from Rage could drop in and take the focus away from the old Fallout factions. Time will tell.
True, but they had the science to back up their claims in Fallout 2 proving that their isolation aboard the oil rig kept them pure, while after just one generation of living in the wasteland the Arroyo tribe was heavily mutated. In Fallout 3 the Enclave should be just as "mutated" as the average wastelander since at least one generation has passed since they became stranded on the mainland. The Enclave should be able to come to this conclusion by simple logic, it doesn't take a rocket scientist, and the Enclave probably had several of those at Navarro.
No! Why should the Enclave just had luck to be on the oil rig when the bombs fell? Probably they used Enclave vaults and after some time they used their vehicles and tech to migrate to the oil rig - or they had a deep sea vault beneath the oil rig. They definitely wouldn't have hidden at the oil rig while the bombs fell, because one bomb at the rig would have blown them to eternity like in FO2 endgame.
So it's rather the Enclave anti-radiation and FEV-filtering tech that allowed them to stay pure. The scientist in the Enclave in FO3 are in biohazard suites to keep them pure and the soldiers in tesla suits are protected too. There are some design errors like the officers and autumn being unprotected (because its more cool), or power armor giving not primarily rad and fev immunity, but basically it works - the Enclave tech is keeping their members pure blooded. The look down upon the vault members, because they are their experiment rats/slaves, thinking they own them. The higher officials of the Enclave even sacrifice their own people.
So the pure blooded principle is purely scientific - it's not being you have to be born inside the Enclave. But who outside the Enclave other than vault members had the chance and tech to stay pure blooded? So it appears you must be born inside the Enclave.