I have been with the series from the very beginning. I was very sad to see the fictional representation of America after the apocolyspe turned into a band of brotherhood of steel bandits. I understand the desire to keep the franchise new and appealing to the younger generation but to give them a small side quest in New Vegas did a diservice to greatness in the old world. Seeing as how you gave the opportunity for the player character to join the evil side in New Vegas (Legion), I thought it would be a good idea to make them a large faction in the next title; perhaps a one that is less bent on domination and ethnic cleansing, and more about the original documents that made America great in the first place, the US Constitution.
I realize the comments in the forum seem to relish the idea of a former government with deminished affect, but considering the time period this game is linked to; I think perhaps you should add a city on the moon in the next title which the enclave hold their real seat of power. The enclave bases on America had to get there fresh stock of troops from somewhere. Perhaps the city was built before the war to house the uber elite people and their families of the world at that time; that being bankers, business owners, politicians, professors, etc. This way, the military outposts located throughout America are more justified for there size.
Perhaps as the cities expanded from the families, different social groups began to form. These could be the greedy business owners having there own desires for how the Enclave city should function, to the academic minded people who have there own thoughts of how the goernment should function. Lastly, you could have the political minded people who have there own ideas of how the enclave should function. Maybe you could emphasize the people of the enclave's hatred for corrupt and greedy leaders and have the player character influence the political direction of the Enclave by having certain politicians, judges, bankers, professors etc. killed. Think about it. In the second game, the Enclave had an academic approach to solving the problems of the waste. In the third game, the enclave had more of a greed based approach of gaining control. This could be used to justify the unstable form of government.
This is not to exclude the people of the waste land on earth however. I think the enclave, the NCR, and the Brotherhood of Steel should be at war with each other and the player character should have the choice of influencing which faction gains control of American territory... or destroys it. The enclave could still have their prejudice against mutants in some of or another but they could at the same time seek to gain gain influence over the people of the waste and have them adopt their side. We known what the NCR's ideals are and that is a good idea for why they seek to control more American territory. The Brotherhood of Steel could seek to remain in the background of the war and use the war to further there own traditions of monopolizing technology. I think it was a bad idea to have them join the NCR as highway patrolmen. In the next game, perhaps you could elude to the idea that the Brotherhood is Steel has a firm grasp of Helios One and that they use the technology to reinforce their already hidden background position of the war.
Anyway, this is far from a complete working concept and I welcome any further imput to make the idea more tangable. My only request is that if you decide to take this concept from those that positively contribute to this idea, then I ask that put this in the original game and not meerly in an addon.