The BoS from FO3 is a different brotherhood. Lyons defy the ideology of the Brotherhood from the West by helping the people of the Capital Wasteland, fighting the good fight and I like Lyons for that. That is the brotherhood I love not the brotherhood Maxon and the other elders has. Though I admit, I do have a hard time in New Vegas, currently siding with Mr. House, and I can't seem to hold the idea that I have to destroy them even though I know they were not Lyons' BoS. Maybe because of Veronica, or maybe because when I think of the Brotherhood of Steel, I think of the one from the Capital Wasteland, not the technology hoarding ass other Fallout franchise has.