Hrm. Good question. Simple answer is make it like Morrowind but with Skyrim combat and and graphics. More detailed, I'd say...
1. Change the level scaling. Have NPCs and monsters fall into brackets so that beggars can only vary from level 1-5 (for example) whereas dragons go from 15+ (just an arbitrary number there). That way, when I'm high level and a major booty kickin' dude, I actually can be. Leveled loot should also be changed. I like the idea that if I'm really clever and lucky, I might find a daedric item very early. Likewise, if I'm robbing random commoners late game, I'm not gonna get ebony longswords.
2. World size. The largest city in all of Skyrim has one clothing store, one general store, one smithy, etc. It's total population is probably around 100-200, maybe less. The total population of Skyrim is probably quite a lot less than 10,000. It takes maybe, MAYBE a couple of hours to walk the entire width of the kingdom. Some hold capitals have less than half a dozen homes in them... I sure wish that instead of all of Skyrim, it had been just one hold done in more detail. Then you could have a single, huge city. A few good sized towns (each bigger than the current cities), and several villages. It'd effectively be the same, overall, except it'd make it seem far more like a real world instead of...Fable.
3. Magic. The number and diversity of spells in Skyrim is astoundingly, shockingly low compared to earlier Elder Scrolls games. I was displeased with the falloff from Morrowind to Oblivion, but it wasn't too terrible, just a bit annoying. Now...wow. Let's just say I am woefully disappointed in Skyrim magic. Though the dual casting is nice.
4. Jack of all Trades Characters. In previous games, you could (over a very long time) master every ability. Now it's impossible. The skill system is now more interesting with perk points and all, but it's far less robust, and means that a single character is, ultimately, going to be limited in what they can do. Frankly, I'd prefer if you could get perk points forever...just make them take exponentially longer to get after a time. Again, robustness paired down to make way for a sleek, cool mechanic. Add the robustness to the sleekness or the sleekness to the robustness, and I'll be thrilled.
5. More detailed interaction with NPCs. I was dismayed that one of the Jarls came to be my enemy because of the civil war even though they were neutral before. I sure wished that I might be able to convince them otherwise. I was terribly upset that members of a certain faction that I loved from previous games demanded that I commit genocide despite there being many good reasons not to. Though there were no options to reason with them or even try to convince them to see things differently. I wanted to make Markarth a better place...but all my efforts seemed to do quite little really. Bascially, NPCs seem less like characters than in previous games, and more like quest mobs.
6. A little more logic and stronger requirements. Basically, it seems odd that I can be named a thane in less than a week after meeting a jarl. It seems odd that I can become the archmage of the college of magic while only ever having cast a single light spell. It seems odd that the entire civil war could be fought and won in a couple of months (and that only because of traveling back and forth from quests). And yet I can't buy a house with being a hero of a city? How do all the other folks get their houses? (granted, most towns don't have very many...) And it just seems odd that all guards know which of your things are stolen goods and which aren't.
Overall, Skyrim is a fantastic and utterly beautiful game. But, it's also disappointing to me. It (the TES series) is becoming more mainstreamed which means more profit and more budget, and that's good in that it gets better voice acting, better graphics, better this that and the other. It truly is a gorgeous game with fantastic sound. And it IS quite fun. However, it's also the sort of game that I play furiously for a month and then put away forever rather than being a game I continue to come back to year after year. I can say with confidence now that Skyrim has become a triple A title like Battlefield 3, Modern Warfare 3, Fable 3, etc. But that isn't what drew me to the Elder Scrolls series. *shrug* But whatcha gonna do? (Oh, right, go back and play Morrowind!

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