I think the problem lies with ultimately the indecisive nature of how the BOS is perceived by the franchise. Because we can blame Bethesda how much we want for making the BOS the "center" but lets not pretend that this was already starting with Fallout Tactics and Fallout Brotherhood of Steel...I mean, people can deny it but Interplay made those, no Bethesda to blame.
Interplay clearly wanted the BOS to be more than just a faction ultimately. Given how they were having the BOS in other chapters where they could prosper better than back in California does show that Interplay was also heading to the direction Bethesda set the BOS in.
I will always be in the camp that says that Lyons was doing the smart thing by adapting the BOS into something else because their original doctrine could only take them so far until they basically enter at war with the rest of the world. F4's BOS seem almost like a course correction from Bethesda because they were tired of people complaining "not my BOS" constantly.
Well, the BOS is now closer to how they were in the originals, except they have unmatched power, and its god damn awful for everyone. Again, there is almost a sense of spite on how the BOS is now...but then again, it could be just Bethesda doing a "be careful what you wish for" type of thing. Fans wanted old school BOS and they got it.
I think Bethesda are slowly re writing the Brotherhood to replace the Enclave in future games. They seem to get less morally gray and more extreme and comically genocidal with each entry.
Part of me wants to believe that this is maybe intentional. Kind like commies fighting Nazis even tho they turn out to be even worse than nazis in the long term.
An institution like the BOS with a lot of power and little adaptability will always lead to evil sooner or later. Especially when you can just shout "ad victoriam" to reassure your guilty mind that you are a noble knight and not a techno-fascist raider.