Level scaling is the number 1 thing. Some enemies should be hard, some easy. All types of armor and weapons should be available from the very beginning, although may not be accessible until you're a higher level, or somehow get lucky and fight your way through at a lower level. A bandit should have the same stats/equipment at level 1 as level 100. If a player has to retreat and come back to a certain quest at a later date so be it.
I say don't make stealing so clear cut. Do it like in Morrowind. A player would have to use common sense as to whether something was able to be taken or not like in real life. If it's not yours, don't take it, or there may be consequences. That way if you take something of someone else's it wouldn't appear stolen in your inventory and/or want to showcase it in your house, it wouldn't say "Steal *item*" when looking at it. And you could sell the item to anyone except the person you stole from. That is just something that bothered me in Oblivion and Fallout. And definitely no "karma" loss, or anything like that, cause who would know that you stole something?
I say get rid of quest markers, and all compass markers. In Morrowind, you had to take time to search for the person/place you wanted, which in turn often led you to secret places, caves, camps, etc. Gave you a better more realistic interaction with the world. As for the compass markers in Oblivion that show where ruins, caves, etc are I want that gone. Makes the vast world much smaller, because you don't have to search for a hidden cave or ruin. It's on the compass. There is no element of exploration, no sense of accomplishment when you clear out a hard to find cave and there was a nice reward inside.
Remove level scaling, remove fast traveling (have teleport spells and travel services in the towns instead).
Remove the quest marker (give better quest explanations instead).
Remove the persuasion and lockpicking minigame (or improve the system significantly).
Remove the constant effect on all enchanted apparel, and cast on strike effect on all weapons (let people choose what they want when they enchant, also put cast when used back into the game).
Remove the skill perks at levels 25, 50, 75 and 100 (give us skill perks, but obtainable by quests, achievements, and skill trainers).
I agree on the fast traveling. Teleport spells and Travel Services to all major towns and some non major towns. But definitely teleport spells.
I agree on the persuasion minigame as well. Morrowind's persuasion was much better, it had no idea how to even use the Oblivion one. And didn't feel like reading instructions on it. So I hoping for Morrwind style, or something new and actually creative.
As for the lockpicking minigame, I'd say use the Fallout style lockpicking. Perhaps make it a bit harder? I thought the Fallout lockpicking was really cool.
I agree about the spell scroll thing, but it's not a big deal to me, I can see it coming in handy for a begining character with low stats, needing some levitate(if it's even included) or some lockpicking. And I definitely agree on the potion overlapping deal, a throwing potion for "on target" would be cool, and make a hell of a lot more sense. Just treat it more of a weapon rather than an aid.