The fighters guild (or Compainions) Should be corrupt. A few of the higher level quest givers should dish out dirty jobs Such as assasinations, Hijacking skooma shipments for mob bosses, Crushing (honest) competition and so on.
The thieves guild Should Realy have jobs that involve stealing or sabotaging Things from GOOD people. Not evil Guards or Cults. They should not care about murder on most missions. There should be a few missions where the player steals from an [censored] but there needs to be ballenced
The dark brotherhood.. Firstly..shut up about sithis. The db is supposed to be a secretive order of assasins.. Not loudmouthed Cult that does nothing but live in a dungeon under an abandoned house! Like the theives guild.. I want a mix of assassinating [censored]s and good people. There should also be Good reasoning on why the person hired the Db
Mages guild.. I am happy to collect mushrooms.. i wouldnt mind Giving someone An evil book to learn from. I do mind a faction war.
Necromancers/Conjurers- It always bothered me that these guys dont do anything Productive with their undead. Personaly id make them Cook,Clean,provide entertainment, help me in my studies and so on.
If a necromancer told me that they would make my corpse dance... i would ask them why. I dont expect a "cause im evil, killing people to raise their corpse for Guarding my lonely cave makes me happy" Realy i wouldnt mind A necromancer mentor.. WHY CANT I HAVE A NECROMANCER TEACHER? Necromancers are obviously going to Have Reasons for Being weirdo's in a cave and id like them explored
As for The church.. You should have nice missions like going on crusades against bad daedra and undead, Converting people to your faith, helping people etc. You should have bad missions. Like assasinating a heretic or Destroying A group of people with an opposing faith.