Ok first off I would like to congratulate you on your amazing work. Morrowind is a huge nostalgia trip for me, I still remember the wonder of playing it for the first time on Xbox as a child and so far from what I have seen from your beautifully crafted previews, you have recaptured this sense of amazement.
One question though, what have you planned for travel between Skyrim and Morrowind? Correct me if I'm wrong but from what I've read in the forums you can travel between these two provinces instead of creating a whole new game where only Morrowind is assessable which I think is great.
The only problem I have is that the events of Morrowind occured 200 years earlier than those of Skyrim so I believe that catching a boat from Windhelm like in the Dragonborn DLC wouldn't make much sense.
This is were an idea of mine comes in. If you already have this sorted then that's fine with me because I know you will do an amazing job. Also if you have all ready made it clear what your plans for this are you have my apologies for bringing it up again.
Anyway, my idea is while playing through Skyrim either in Eastmarch (probably near Dunmeth Pass) or in the ash wastes of Solsthiem you come across a Ashlander yurt. Inside the yurt you meet an Ashlander wise woman (who is something cliché like the last of her tribe after escaping from the eruption of Red Mountain during the red year or something along those lines). upon talking to her she tells you the story of the Nerevarine. She then offers you some freaky potion from a bowl which you drink which causes you to fall asleep. The screen then cuts to an intro video like the one of Azura speaking to you at the beginning of Morrowind and/or a loading screen displaying some of your amazing 3D models. And then you wake up in a boat next to Juib in Seyda Neen and relive the steps of the Nerevarine.
You then have the option to travel back between Skyrim and Morrowind by entering the door of the ship in Morrowind and returning to the wise woman to hear more of her story.
If anyone has any critiques or an entirely better idea feel free to voice them ;)