I don't see any reason the Fighters' Guild wouldn't be vigilante's. They should be. Ethics conflicts should be part of the internal strife of the Fighters' Guild.
I agree with this like a lot.
I really do not want to see a bunch of polar opposite factions. "If you're a goodie join this one! If you're a baddie join that one!" It's so contrived and unnatural. I'd like to see internal struggles, power grabs, etc. Not everyone should be on the same page or have the same goals in mind. Members of a faction should exhibit blind ambition, short-sightedness, stupidity, nobility, loyalty and betrayal, and everything in between. This isn't Disneyland, I want some depth.
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Not so familiar with necromancer lore, but I'd really rather not see a necromancer guild. It seems so trite and corny. If there is to be a joinable necromancer faction, I'd like it to operate more as cells. Something closer to the Telvanni hierarchy than the Mages Guild. You have the opportunity to assist and study under a singular necromancer. You perform tasks and chores for him/her that they are unable to handle. Thigns like dealing with the public, securing specific materials, ingredients, literature to aid in study.
You may act along with other Necromancers, but any cooperation is temporary, only used when there it is clearly mutually beneficial. You might collaborate with other necromancers on research, trade information, band together in times of inquisition. But you are not allies. You'd just as soon stab another necromancer in the back and steal their notes as you would aid them.
The system should be underground. Invisible to those who aren't a part of it, and those who are become aware of just how far the web reaches.