I know Bethesda doesn't like bringing up Interplay and their games due to the animosity between them but Bethesda have stuck almost entirely to the original Fallout canon and New Vegas is bascialy a direct sequel to (the cancelled game) known as Van Buren. Originally there was no way the NCR could win the NCR-Brotherhood war, either white peace or total brotherhood victory, however New Vegas say that the NCR won the war. Howcome? Fallout canon, including NV, states that the war lent heavily in the brotherhoods favour.
Bethesda and Interplay are treating the BOS very differently, to Interplay they were a good people who made neccesary sacrifices to preserve order and the technology of the past but with Bethesda they often come across as the bad guys, they seem like greedy hoarders who reject all others.
PS Midwest Brotherhood don't count, they've always been evil. And Lyons Brotherhood are not real brotherhood, in talking West Coast BOS.