Elder-Scrolls Series in general: More choices. Not necessarily moral choices, but each instalment has felt more and more like a Roller-coaster experience.
The Great House Dagoth mod improves Morrowind's main quest so much by making joining House Dagoth possible, as well as making it possible to betray Dagoth Ur and become a god alongside the Tribunal, or betray the entire Tribunal as well as Dagoth Ur and become the sole god of Morrowind. Or you can even commit a Heroic Sacrifice, and destroy the heart to kill both yourself and Dagoth Ur.
All of this whilst still fulfilling the deliberately poorly worded prophecy of Nerevarine and staying completely within the themes of the game to the point it feels like a natural part of the game.
That kind of thing, that you can do this kind of thing but only if you are smart enough to realise you can do it and not just blindly follow the quest marker, is what Elder Scrolls is truly missing. What Role-playing games in general lately have been missing.
Oh, and level scaling: Stop it. I much prefer Morrowind's static world to Oblivion and Skyrim's approach.
This is all good things.
That said, do you have a link to the mod in question? I might be able to get Morrowind soon and yeah.