Doesn't make sense to me to have the BoS as allies if you go any route at all.
Even by allying them with NCR, they end up taking all the power armor.
What would they want if you sided with House, or went Independent? They'd want to have a look at those robots, now wouldn't they?
to be honest, there really should have been the option to subjugate the entire brotherhood because of your superior military power.. i mean, seriously. 15 guys in power armor versus hundreds of securitrons mk2?
anyway... the inability to utilize the broterhood in houses storyline feels completely invalid. if anything, mr. house would be very open to abusing the trust of the brotherhood.
so you wanna check out my robots huh? sure, after you fight for me at the hoover dam. and i promise i won't kill the survivors.... nope, i certainly won't be doing that.