Skyrim had that thing where every cave you go into there is a generic story told inside by a letter on a dead body. The world was full, but it was filled with generic stuff like that, utterly uninteresting after you realize what's going on. The main story was not strong and the balance with the only storywise mighty dragons that were ingame quite weak was completely off. Auto-leveling of quest items made quest rewards worthless.
Oblivion was unplayable because of the extreme auto-leveling, if you weren't extremely lucky with how you played it or fixed it with a mod.
Morrowind had none of those flaws. There was auto-leveling (mainly leveled lists with a small range, iirc), but the effect was small and felt organic. And the world is less filled with generic bs, no shoved in story told in every cave. The lore presented and the atmosphere was awesome, with the local gods and their path to power, the nerevarine part of it and the diverging perspectives (though a modern game might have used that for a non-linear story, which MW completely failed to do).
I also got the impression that the stories written in the ingame books were a lot more interesting in Morrowind. In the later games that got too boring fast, in Morrowind I actually read most of them. Might have been me becoming less patient over time, but I read somewhere the authors changed, so not impossible my impression is valid.
Graphics are obviously worse, Quests can be a bit off - especially the guild quests. Not only are they strange in what they ask from you, breaking immersion; Like in Oblivion and Skyrim following those quest lines and becoming a guild leader does not amount to much. Only do one, then it's okay. Some game mechanic can be broken rather easily, but if you don't search for ways on Youtube I doubt that's an issue when just playing - but Oblivion and Skyrim are a bit more stable there.
I liked Morrowind best, but it was also the first I played and the one I wrote simple mods for.