1) Skyrim needs Oblivion's "no psychic guards" mod. I took Faendal from Riverwood up to the Sacellum of Boethiah and sacrificed him to the Prince of Plots. There was absolutely no one there to see us since I'd already killed off all of Boethiah's worshipers, but when I returned to Whiterun the guards tried to arrest me for the murder. There were no witnesses, there was no way for them to know I was the one responsible and it wasn't some random bandit somewhere. Another similar incident, I was following a treasure map just outside Whiterun and I passed through a farm. Since I needed to gather some souls for my enchanting, I decided to start killing chickens. I found a nice dark spot to keep the farmers from spotting me (I was about to start killing their livestock, after all) and shot a chicken with my soul trap bow. I immediately got a bounty in Whiterun despite the fact that I was hidden so the farmers couldn't have identified me.
2) A tweak of AI when you're trespassing. I broke into the Hag's Cure in Markarth on a numbers job and the shopkeeper spotted me. I immediately found a dark corner and my status switched to hidden, but instead of looking for me and eventually giving up like hostile NPCs do, the shopkeeper walked right up to me, stood staring at me, shouting "you need to leave" even though the sneak cursor said I was hidden. And then she called the guards (through several feet of stone and a heavy dwarven metal door I might add) and they came running in, ran right up to where I was hidden and tried to arrest me while I remained hidden. And quite often when I break into a shop or house the owner follows me around, yelling "You need to leave" even though the sneak cursor says I'm hidden the entire time.
3) The heavy armor perks need to be tweaked because right now they're absolutely dominated by the light armor perks. It takes 10 perks to max out light armor and all of the perks kick ass: increased armor rating, weightless light armor, increased stamina regen, AND a 10% chance to dodge attacks. It takes 12 perks to max out heavy armor and some of them suck: increased armor rating, weightless heavy armor, and 10% chance to reflect an attack back on the attacker are great, but halved falling damage, 50% reduced chance to be staggered, and extra damage when unarmed are all worthless. I mean, if you fall off a cliff then you're doing it wrong and who in their right mind goes around in badass heavy armor without a similarly badass weapon and/or spell in hand?
4) A mountain-climbing mod. I'm sick of the game deciding an incline is too steep and forcing me to stop even though I could climb it easily if the game would just let me climb instead of run. People have scaled Everest, spelunkers can climb across ceilings, I should be able to reach Shearpoint without having to circle the mountain looking for the god-damn path.
5) Water combat. Maybe I just haven't discovered how yet, but if I'm attacked by a slaughterfish while swimming I want to at least pull out a dive knife to try and defend myself.
6) A slight "realism" tweak. I don't care how much health you have, if I put an arrow through your eye you shouldn't be walking away from it. Also, if I sneak up behind you with a knife I'm not going to stab some random spot that lets you turn around and fight back, I'm going to slit your throat (this wouldn't bother me so much if the game didn't have two different "sneak attack throat-slitting" animations already programmed into it).
7) I'd like it if masks didn't cut off my Argonian's snout. I mean, no Argonian version of the Dragon Priest masks or the Nightingale hood seem like design oversights.
8) I find it strange that my Argonian has a pair of huge horns on the back of his head but when he puts on a helmet they disappear, so some mod that keeps my character's hair from being replaced by the helmet would be nice.