So, in order to balance it, they made the technology that made tanks obsolete commonplace and weak? No, i prefer Power Armor indestructible and rare as cats, that itself was balance, the modern age of video games, aren't games supposed to be fun?
There is the simple, if not realistic, solution. If the Brotherhood were made unlootable, there would be no need for balancing, and the Power Armor could be made much more powerful. I believe deathclaws should be made extremely powerful because they can't be looted for powerful items. If the Brotherhood couldn't be looted, it would solve the problem and they could be made extremely powerful as well.
But from a story perspective, the Brotherhood isn't nearly as unstoppable as it used to be. That has to be reflected in the gameplay. If anything, the Enclave Power Armor should be nearly indestructible.