If I remember correctly, vanilla Morrowind had a system where the PC could choose from three sites, and house designs. Later as gameplay progressed, the selected home was improved, to include addition of buildings, static items, and NPCs.
In the vanilla Bloodmoon expansion, there were a series of quests for Raven Rock, wherein, the PC performed quests that helped in the development of the Raven Rock Colony, to include NPCs, a choice of lots for the PC's personal home, and finally the completed construction of the home, to include static items, as well as plenty of storage.
So, to my way of thinking, it is well within the lore of TES for there to be lot choice, type of home, and gradual development ofthat real estate.
And of course in Oblivion, there were several homes available. One could choose one or all.
However, it has been a while, but it was something like that. None of this required any DLC, or mods.
You are correct, there were 3 sites but it was the Political House Faction you sided with in the game that chose the location for you in Morrowind.
Then there was a number of quests that were linked with your progression within the faction and the initial building of the house and its development.
This I think would be great to implement into Skyrim, If you can join one of the Nord Clans involved in the civil war, and have ahome built for you in their respective town/village where you have to complete quests and raise in the ranks and collect materials to build it and develop it, until becoming the chiefan and building your own mead hall.