lol I agree. Npc Driven Factions should be a great role playing experience, if there is really no point in joining them (no quests, no advantages, no immersion, etc) then they shouldn't be necessary to get professions... seems like common sense tho hate to say it but even as a Slaver, slavers still attack you (atleast from the last wipe dunno bout now)
A good idea for npc driven factions could be like discounts in the town or access to better equipment on vendors in that town, the ability to do unique caravan runs for the BOS etc going back and forth to really dangerous zones... Raiders doing "loot runs" ex. Travelling from Raider camp to Broken hills to back searching the wasteland for critters, merchants and blue suits lol... a ranking system if you join a military based organization ex BOS start as a recruit for ever quest you do or items you bring in your rank goes up and can possibly advance giving you the opportunity to purchase better gear with a 2% discount for every rank you got up. Fights for towns, escorts, etc, etc.
This could also help seperate the quests making the player have to get to the rank of Captain for higher paying jobs etc. You really got to make it feel like your part of that faction doing brotherhood stuff or raider stuff to mordino stuff; selling drugs from town to town or collecting debts for the mordinos) its all about immersion or else its just useless filler ala Fallout 3 and its crappy never ending useless side quests.
I could actually talk about this ALL DAY but lol these are just some basic ideas that would make the game even greater! Aniketos has a great point