there are some elements that i can't put apart from the fallout world, to me those elements are for example the vaults, enclave, brotherhood, mutants
I would like to see those factions always present in a fallout game ... but in a dynamic context and not often as a ctrl c + ctrl v from old storyboards. I mean factions should evolve ... build history ... in that aspect i am in favor of what Bethesda did for the brotherhood, if the brotherhood is nearly a collapse its reasonable that many sub factions would emerge from the drowning core, considering it's lack of capacity to keep unity inside the order.
as for the midwestern brotherood, i read at the fallout wiki that its considered semi-canon ... due some aspects f3+ we can assume that fot happened (for ex, the rogue bunker of the midwestern bos in Chicago). All signs point that if a calculator ever existed the menace created by it's forces was only regional. Also much of the resources build by the midwestern bos was drained by this conflict, reducing greatly the order's power and influence, i guess that info can be considered canon ... but since there is no official note about it, there can only be speculation ...