I never understood why anyone would even bother trying to do Morrowind in either oblivion or skyrim. No medium armor, no spears (or even animations for them), no alchemy. Skyrim itself doesn't even have spell crafting. The enchanting in both games was much more limited than in Morrowind too.
This was my first thought when I first heard people were doing this. You don't have access to really alter the character system that much in any Bethesda game through mods, so you're stuck with that system that the base game gives you for the most part. You can tweek it, rename things, and so on, but you're stuck with the fundamental system that's already in place. There have been quite a few attempts to give Skyrim a more traditional Elder Scrolls skill system, but those are typically things outside the actual system that just modify the player as opposed to being able to do it directly. There's really not a good way to do Atheletics or Acrobatics in Skyrim, which was a huge part of playing a sneaky theif type character in that game.
You'll be able to make the story, and there's that expansion which added some Morrowind assets to the game, but the gameplay itself will be as shallow as Skyrim's. As you mentioned, there's no Medium Armor in Skyrim, so you're stuck with either ignoring that it exists and ditch all those armors OR you'll have to shoe horn those armors in to either Light or Heavy Armor, both of which have Perk Trees which may not make sense for the Morrowind idea of Medium Armor. Same thing with Spears. About the only caveat to the spears thing is that I don't recall any unique or special spears in the game.