For me, it would have to have something to do with radiant random AI being more clever and radiant NPC's generating out of nowhere, along Skyrim's border's at random. They would then be able to build small shacks and maybe rarely small communities(chances of this happening would be even higher if you were a khajiit), but this would probably have to be a scripted locations(thankfully Skyrim is pretty large, so there's plenty of locations where the radiant AI could play around with).
Second feature that I'd like would be to have the possibility to conquer caves and maybe even dig deeper than how big the cave originally is using mining pick somehow. This could probably require some physics engine remakes however and im not sure if it would make the game feel a bit too minecraftish.
Third is to somehow allow us to join certain non-joinable factions and make the game have as many factions as Oblivion and expand on it. Want to be a bandit? If you have enough in speechcraft skill, you could perhaps approach certain fortress' bandits and challenge or negotiate with their leader. Either you kill the leader, or do like 2-3 small quests for him and then last quest is to overthrow him. Or, want to conquer the fort for your own needs or make it an Imperial Guard outpost? No problem, and refurbishing options would be avalaible as well.

Like a bunny!
I hate it