I used to think that only some minor things were cut from the game. Originally, the Blight was supposed to spread, but was cut because it couldn't be done well, and you were supposed to be able to join House Dagoth, but that was cut for time. And maybe these cuts were for the better. A spreading Blight would force you to do the main quest quickly, and having the Nerevarine join Dagoth Ur in lore would lead to another Dragonbreak excuse.
But then, while searching for empty places in the game to add buildings to, I noticed something off about Ebonheart. You have a trading company, a temple, a castle, and an inn, but no houses. And then you have a road leading South from Ebonheart down a large peninsula, but there's nothing there. It's a road that leads nowhere. Is half of Ebonheart missing? That's not a small detail. What else was cut?