The fatigue system can go, it serves no purpose other than to slow a pc down.
Needing to sleep every time a pc levels can go, just let me level when it's time.
Encumberance can go, just give me a backpack and whatever I can stuff into it is what I can carry.
Loot that scales with pc level was one of the worst ideas in gaming history.
3D rotateable views of inventory items. Sorry Mr. Howard but this one's superfluous before it's even released. Huge waste of time.
"Go Fetch" quest lines. I've taken to killing any npc who even hints that they want me to go gather some easily found resource and report back.
A pc should never be a spectator for the final battle of a game.
Things masquerading as DLC's that should have just been included in the game or patches. IE: Horse Armor. If you want us to pay for something then at least present something worth buying.
Easily abused leveling system. What I mean is skills like acrobatics where I can just jump up and down on a tavern table and gain levels. With many TES games you can get to level 20 or so and never leave town. I'd like to see a system that makes at least a little sense. Perhaps it's time to go with an exp point system. *gasp* (I realize Acrobatics might not be in Skyrim, it's just an example of how easy it is to exploit TES leveling system.)
Nirnroot quest. While I didn't mind having a quest like this the reward was questionable at best. risk + time = reward just didn't add up here.
Respawning containers can go, heck you could even remove them from the world once looted. (Containers in pc housing should remain but not respawn their contents)
Stealth. No really. It doesn't make any sense that I can sneak and not be seen while standing right in front of someone. Just because I'm crouched down being sneaky doesn't mean they shouldn't see me. Either make a system that makes sense or just get rid of it.