They'll both probably be in Skyrim to some degree. I'm expecting that one of these will continue the more public, commercial role that the Mages' Guild served in previous TES games whilst the other one sounds more like a sort of secret order or Inquisition working on behalf of the Imperials. I'm hoping for some pretty interesting conflicts between the two as we saw with the Tongs in Morrowind. Unfortunately, I think I heard that they were both Imperially sanctioned so we may not see any large scale disputes between them. But I could imagine them both trying to overstep their boundaries and seize control of the duties of the other.
What do you think? Will we be fortunate enough to join both, or just one?