The usual guilds, of course ; I would particularly appreciate that both the Dark Brotherhood and the Morag Tong should be present.
After all, destruction of Vvardenfell, we know a lot of Dunmers went to Skyrim, right ? And maybe expand on the Mage's Guild problems.
Otherwise, politics/religion related guilds. Daedra cults is not a bad idea ; the interaction with more traditional cults should be fun. Remnant of Houses, what with the aforesaid Dunmer influx, why not.
Not so much the other type of guilds you mentioned. Thing is, I don't wish so much for number of factions, as I want more complexity and inter-guild issues, alliances, mistrust and whatnot. As it has been often suggested, why not join one to do undermining work for another ?
Seems a bit chaotic, but it's civil war, after all : times like these, every little faction is out for blood - mere survival or expansion of power.