For instance:
Temple Faction sub factions <<
- Groundskeeper (name still in the works): your duty is to clean out ancestral tombs of invasive NPCs or creatures, and possibly to add new guardians to the tombs. You'd have an item that makes all Undead (and possibly some daedra?) passive toward you because you are not an enemy, you are an ordained official come to uphold the sanctity of the ancestral burial chambers.
- Armiger: your duty would be to hunt down Blight monsters that escape the Ghost Fence, and to make forays into the Fence to cull the burgeoning blight beasts and 6th House monsters. Other duties might include special missions from Vivec himself.
- Ordinator: duties include hunting down heretic Daeda worshippers and clearing out daedric ruins of such heretics. Other duties (before Main Quest completion) would involve apprehending heretics (Tribunal-deniers) and bringing them to Lie Rock; patrolling the Vivec cantons and apprehending criminals, clearing out the waterwork's daedric shrines; dispatching any creatures that enter the lower cantons from the waterworks.
- High Ordinator (Tribunal): an "upgrade" of the Ordinator, I'd think this would be less a separate faction and more of an "advancement," perhaps offered by Almalexia before she goes completely bat-crap crazy and tries to kill you. You would never be a "Her Hand" that wouldn't make sense. But as a "High Ordinator" you would act as a guard in Mournhold; track down criminals, smugglers, heretics. Other missions could involve clashing horns with Helseth's Royal Guards, doing Temple-things over on Vvardenfell, etc.
Imperial Legion and Cult
This would utilize the unused http://www.uesp.net/wiki/Morrowind:Imperial_Knights faction, and tweak it so that the player could pick a specific http://www.uesp.net/wiki/Daggerfall:Temples to pursue. Missions would be for the glory of your gods and emperor, and butt heads or negotiate with native Dunmer officials and prominent figures. Other missions would tie in the Cult and Legion members and areas - example, protecting or establishing a new Mission center. I'd need to think about missions that would be suitable.
- Census and Excise faction : This is an unused faction, but totally set up with ranks and brimming with potential for missions. You could track down smugglers, corrupt importers, impound contraband, collect taxes (and try not to get killed), take a census, etc. I'm not sure how to implement it. Of course it would only really make sense if someone in the Legion or Cult joined, but the favored skills for C&E would need to be vague enough so that they'd overlap but not exclude the required favored skills for those two major Imperial factions.
Great Houses <<<<
- Royal Guards: House Redoran and House Hlaalu members could be invited by Helseth (or the guy in charge of the Royal Guards) to become a Royal Guard. Missions would involve catching criminals and the like, but also things like butting heads with the Temple officials and running "special" political missions.
- Commona Tong: only available to House Hlaalu members. Missions would be typical of a crime syndicate: smuggling, subverting Imperial law, theft, money laundering, political power-playing and blackmail, etc.
- I can't think of anything else at the moment. I had this idea for "specialties" within House Telvanni. One would involve talking with Lesser Daedra and being involved in their politics, making business contracts, etc. Another specialty might involve unconventional research (enchanted items, alchemy and ingredients, new spells, etc.).
Just some ideas I had. Discuss!
EDIT: I know quests and factions aren't easy to make. So, this is more of just a big idea I have. If anyone wants to try to tackle one of these, I could try to write up specific quests and maybe some faction guidelines/lore.