I enjoyed this system, it allowed me to change the world how I felt necessary, and set up shop wherever I needed to. Yes, its true that if I cleared every dungeon in the game, i'd be out of places to explore - thats a fact of life in the game, however I never reached that point! I never played a character to the point that there were no longer places to explore, loot, and take over.
In Oblivion, if I went to take a home that I liked, I could remove all the loot, (and trash most if it - see http://www.gamesas.com/index.php?/topic/1164057-junk-items-have-value/) and place all my own items. This was fine, until I happened to be away for 73 hours - at that point every item in the house would respawn where it used to be, even if it meant spawning on top of and displacing all the other items. Strangely, the NPC who was "displaced" never respawned, meaning the house was entirely useless and empty (minus junk goods) for the rest of the game.
In Skyrim, my alternative would be, at least for NPC owned homes, that items do not respawn and, if they do, the items only respawn if the NPC/NPC's living there are still alive. I do not want to touch on dungeons respawning, because it seems Bethesda has some interesting plans to recreate the dungeon experience as it is, and i'm more than willing to give this a chance.
I'd also like to add here at the bottom something thats been discussed on the forum: No red hand next to stolen goods. The player should be able to determine if they are stealing or not - and if they are unable to, they're going to have to deal with those consequences.