I’ll start this thread off with a thought I had while going through the old documentation.
One of the suggested tropes for the Mages Guild is that they are beset by corruption, with the powerful members pursuing their own ends and letting the Mages Guild flounder as a result. It’s another symptom of the Empire’s eminent collapse.
However, I think this would make them out to be a kind of bleached out version of the Telvanni, which is meh. Plus it also pounds in this notion that the Empire and the Temple and everyone is failing, which is...interesting, but way overused at this point, tbh. Turning the Mages Guild into yet another version of corruption-destroying-the-faction-from-within isn’t good storytelling when we’ve got several other factions with the exact same trope going on (Dres, Temple, Hlaalu, Indoril, maybe Redoran...). Note also how all those factions are Morrowind natives. A better direction with the Empire may be that the Dunmer are falling to corruption, while the Imperials are EITHER the possible saviors, or the scavengers picking them further apart for their own ends (or both).
So instead, what if the direction of the Mages Guild investigating some of the metaphysical effects of the Red Moment? Using this as a center for the Guild, the Empire could once again be cast as the possible saviors or exploiters of the greater calamities going on under the surface of the Tribunal’s collapse. The Mages Guild deals with the magical aspects. Such as: the universal anomolies caused by three (well, four) mortals becoming gods, an entire race going poof, the true nature of the Blight, and the Chimer being changed into the Dunmer. Note, we probably shouldn’t go into trying to explain these things that Bethesda has so carefully kept obcure, but instead muddy the issue by contributing alternative theories for the player to chew on.
This could throw in a bit of a trope of science vs. religion too, which I think could also open up some interesting doors between the native religions (Temple and the Ashlanders) and the Mages Guild interacting. Mages Guild irritating the Temple by wanting to know how their ancestor worship differs from necromacy. Mages Guild irritating the Ashlanders by trying to assign magical theories to their dreamslore. Etc. We could also throw in some very dark stuff, such as a quasi-necromancer of the Guild vivisecting Dunmer to try and figure out why they have ashy skin and red eyes, attracting the ire of Azura in the process. (This particular storyline could also serve as a contributor as to why Archmage Traven took such a firm stance against necromancy in TES4, tying some of these games together.)
Dwemer studies would be an obvious direction to go. I know how their constructs worked was already investigated in a Skyrim quest, but something similar to that perhaps. Or, maybe a mystic of the guild picks up on a trace of Dwemer souls in the Dreamsleeve. (Be aware, I am suggesting this from the point of the view of the NPC: no Dwemer souls exist in the Dreamsleeve, but an enterprising young mage may find something he/she “thinks” is a Dwemer memory and try to capitalize on the maginificent discovery.) The rival of this particular mage has his/her doubts, and the PC is sent to discredit the mystic, but the mystic’s findings are compelling enough the higher ups have been dragged into it.
Another quest arc could be based on the idea of one of the higher ups trying to reproduce the Tribunal’s ascension and getting dragged off by Ordinators before he can get anywhere with it. The Mages Guild decides to help the Ordinators or at least turn a blind eye to it to prevent political blow-ups. As far the theme of being saviors/opportunists, perhaps the blasphemous mage got just far enough in his research to start suggesting the Tribunal’s power was Dwemer based. The Mages Guild then cleverly manuevers the Temple into their debt by saying they will destroy or falsify the damning research before it can get out to the public.
The Mages Guild could also interact with the Dres, calling into question the convention behind their vampiric leaders. This may or may not be the reason the Mages Guild is no longer welcome in Tear. (Also solving the problem of that captial city guild guide thing we had.)
Anyway, there’s a bunch of other ways you could go with this, but those were some examples I could think of off the top of my head to help illustrate what this direction for the faction would look like. TL;DR Mages Guild interacting with native Dunmer magic and beliefs, and poking holes into all the things.