It shouldn't be like that, that's the problem. Have everything respawn except for one's own home, quests, and character accomplishments. Oblivion had the same variables to track as Skyrim, and it never swelled and fell apart like this.
there are modders who are calling for specific changes to be made with the way the game retains memory. I don't know or understand that much of the technical details. it doesn't make sense to me either that the save files are so much more expansive.
the game has to keep track of a lot more than a typical sandbox game that uses tricks like duplicate cars and npc models and such. Skyrim doesn't do any of those. Each individual NPC has it's own scripts. certain things have to be retained by memory, like alchemy ingredients refresh and when bodies 'disappear', a lot of stuff the average player probably doesn't account for but the game engine has to.
There are known problems, at least known by the users and have been posted on the forums. Nirnroots refreshing their light every 24 hours, ash-piles/dropped weapons or fallen items and corpses don't disappear, glitches with npc behaviors, stuff that can be found and patched, hopefully. I'm still enjoying the game and I feel bad for those who aren't able to. Bethesda should fix the game to be able to run on all the platforms they released the game for, that's my opinion.