The main problem of your suggestion is that you dont need to be in a faction for helping it. In others words, how the game can differenciate a REAL lone wanderer and a non gang affiliated character ?
I'm all for the special quest item. The high requirement craft only encourages alts sadly. I guess there is of no question only BoS and Enclave affiliates could wear them. Maybe they could only be repairable in the faction base. As well as the top tier weapons. So one player could only have one or two top tier items. If they are unlootable and untradable and destroyed on drop there is no problem.
Huh, in this case, what are their interest? A CA is cheapest, and with psycho you are as tough as a guy in PA without the agility decrase!No, they are "super high tier" weapons and armors for a reason: THEY ARE BETTER. No interest if you give them malus.
THIS IS NOT BETA THIS IS SPARTA
Oh, I forgot the game was based around an adolescent desire to BE THE BEST. Tradeoffs are more interesting than just being better.