Frankly, you just can't have empty dungeons willy nilly. There is plenty of opportunities that are realistic that allow for dungeons to have residents and items that are still salvageable. It would be better to have every dungeon in Skyrim to be filled to the top with gold and listen to some of the people that think it's unrealistic than listen to those same people raging about how they hate how when you walk into a a dungeons it is empty and they could've done things with that empty dungeon. Trust me, people would say that.
I've started playing Morrowind for the first time, I'm finding loads of NPC's in dungeons, handing out mini quests or having something interesting to say, I think there were maybe two dungeons in Oblivion where I met someone who didn't want to kill me, Fallout 3 was a big improvement in this regard so I'm hopeful they're on the right track.
Well to be fair, Morrowind's dungeons were full of people researching Dwemer ruins, researching Daedric ruins or just lived there because of the way Vvardenfell is. In Cyrodiil, not that many people would want to wander into a haunted fort or Ayleid ruins seeing as how Ayleid ruins are extremely dangerous with all their traps and the greedy treasure hunters trying to kill you to make sure you don't steal any of their stuff.