Numbers. The NCR vastly outnumbered the Brotherhood and wore them down. The West Coast Brotherhood has always been isolationist and every member lost added up. The NCR could afford the loss of men, the Brotherhood could not. They didn’t “ruin the lore” when the ideology of the West Coast Brotherhood (who have been a thing since the first two games) is the same as it ever was and put them in a really bad spot. They never would have had a chance against a force as large as the NCR no matter how much power armor they had. It doesn’t make you invincible.