I'm not sure if this has been discussed or not, but from what I've found on this site so far, when it comes to Skywind there's one thing that hasn't really been discussed very much; Slavery. In fact, slavery wasn't even addressed enough in Morrowind to begin with, which has always irritated me.
One thing that really bugged me was that there wasn't a key for every area with slaves. What also bugged me was how many people thought it was impossible to free the slaves in areas without slave keys (such as Sadrith Mora), and they were wrong because you can just use a control humanoid spell to leads them to an area with a key and they can be freed. So this is what I propose; create slave keys for every area with slaves so there's not such a big hassle in freeing every slave (which was difficult but can be done). I also think that there should be more behind the Twin Lamps faction. I know there's a couple of mods at there that elaborate more on the Twin Lamps.
Another thing that I think should be made possible in Skyrim is the abolition of slavery. When you look at the timeline for the Elder Scrolls. you'll see that Oblivion only takes place 6 years after Morrowind, and slavery was abolished before the events of Oblivion. So naturally, having a questline to end slavery is something that would not only make Skywind more interesting, but it would also be the more lore-friendly option.

Interesting, but I don't know
Interesting, but I don't know how this makes it "more lore-friendly". The fact is that slavery was never abolished during the gameplay of Morrowind. We don't know for certain when it was abolished, just like we don't know for certain when the Nerevarine or Vivec disappeared. Those things only happened in between gameplay events. Sprucing up the Twin Lamps might be a good idea though.
Edit: You know what might be cool, if you add more missions to the twin lamps that ultimately lead up to events where you petition to the Emperor to abolish slavery. The outcome of the abolishment wont happen during gameplay, but one can assume that they had a part in its outcome.