Where did you read this? I don't think it has any basis in reality. The Brotherhood is an organization with its roots in the unit stationed at the Mariposa Military Base just before the war. Their purpose and goal is to collect pre-war technology. So Fallout 3's brotherhood is not only logistically impossible, but it also isn't the brotherhood, as the outcasts will tell you. They're staunchly indepentent and wouldn't accept outside help. They're also kind of at war with the NCR, that's a big part of what made them so weak.
The Enclave is the old United States government. It was founded by high level officials of the pre-war government. They all fled to an oil rig outside of San Francisco as the bombs started falling, and that's where they remain headquartered. It keeps them from being radiated like the rest of the Wasteland, which leads me to their ideology. They view themselves as the only remaining humans. Everyone else has been tainted by radiation. The President tells you straight up that you're not human. That's why they develop a deadly version of the FEV virus to eradicate America of mutants and make it safe for "human" settlement.
The Chosen One destroys the oil rig, and the NCR then destroys their one big base on the Mainland. That should have been the end of them aside from the remnant. The notion that they had the resources to fly all the way accross America with the vast majority of their Vertibirds destroyed as well as their two fuel stations destroyed is absolutely ridiculous.
The new faction that's mentioned sounds really cool. The Commonwealth is an absolutely brilliant idea, I think, and would fit into the lore of the game perfectly, especially considering that Massachussetts is officially "the Commonwealth of Massachussetts". Fallout 3 should have been about them, and I'm glad they'll have an important role in Fallout 4.
The Raiders actually come from the same place NCR camr from. Vault 15. The Vipers, Jackals and Khans were all people who left Vault 15. Although they decided to start stealing and killing people instead of settling down like Aradesh and his group.
Most things in Fallout, especially on the west coast side of things have very believable lore. Like, nothing, if you accept the level of technology at the time seems to be uneblievable. If Betheshda has to resort to a lore that involves a shadow organization controlling everything for their story to make sense, then they're completely incompetent when it comes to storytelling and should quit making Fallout games entirely.