What do I want for future modifications? Here is a list.
More Random Encounters. While I like that Skyrim is mostly open and does not involve a lot of random people out in the wilds, I felt they could increase it a tiny bit. I wanted to see more bandits appearing, maybe even with small migrating camps, in the areas around Whiterun or in the various hills. I want to see more Thalmor Agents walking the roads or even more caravans. Some of the best times where stumbling into a bandit ambush. Would love to see that more often and more dynamic. Maybe that road I walked before now has a group of thugs attempting to ask for a toll, or the Thalmor have setup a small camp just off the road where they are interrogating villagers.
More Travel Options. Really miss the old Acrobat stat. I liked being a crazy guy that could nearly leap up hills. Would also like small spells for doing things like Levitation, or a return of the Featherfall spell. Dragon Riding wouldn't hurt either so we have more options other then a horse, but make gaining such ability decently difficult or at least involve a quest. Anything to make the travel a bit easier without breaking the immersion quality of exploration.
Less Aggressive Animals. Seriously, not every wolf is going to attack a person the minute they get in a short radius. Animals should avoid the player or other races unless provoked, either by extreme proximity or through attacking them. Have a few stay aggressive, but only to keep things interesting, but it shouldn't be nearly 100% like it is now. Having scary things jumping you should be more about those More Random Encounters.
No Wilderness Spiders. The thing I liked about the spiders is that when you went into a spider nest you had this slightly freaked out feeling. I found this feeling of dread occurred less and less as I ran into spiders randomly out in the woods, nowhere near the webbed tombs they made homes. I want running into those webbed areas to remain scary, because you never know when a spider is going to jump out of a crack at you. I don't want to see the spiders unless I am in a dark, cramped web filled room.
More Diplomatic Options. I don't like that, even with high speech, I can't influence the leadership of the various groups to come to terms. I want something that gives more options to end the various conflicts and wars without resorting to bloodshed or direct sieges. The game is supposed to be about the freedom, and I don't feel I have as much freedom as I would like if I can't work towards a diplomatic goal. You can even make it ten times harder then the conflict scenarios, and I would do it.
Ability to become a Jarl, or even the High King. I can understand in Oblivion that allowing the player to become The Emperor would never work in the context of the main story, but this time we are literally the next Dovahkiin, the only other one being Tiber Septim himself. I think allowing us to pursue the path of rule, either through diplomacy or conquest, should have been in from the start.
More Factions. The game already has a lot of factions, but I would like to see a few more appear that should have been open in the first place. Examples. The Thalmor are an interesting faction, and wouldn't mind the ability to join with them on certain characters. The dark elves pretty much all fled to Skyrim, and after being such a powerful, driven kingdom with a lot of strong factions, some lead by literal demi-gods, they don't have a single collective force pushing for their own rights? Would even more more quests for the Forsworn, the Orc Camps, etc...
Better Followers. Make it so Followers can't be killed when marked as a Follower and is immune to all your abilities. Using a Shout will knock away enemies, but through power of the voice you can save your followers from it's devastating effects. Make it so you can equip Followers gear specifically, rather then them auto-equiping what has the highest number. Allow Followers to "auto-upgrade" once marked as a Follower to your level. Lastly, allow the usage of two or three followers rather then one, allowing you to build a "party". If difficulty is an issue, make it so the games auto-calculator for NPC difficult marks you up to an assumed higher level when you have more then one follower, so each NPC will be even harder to kill.
Better Crafting For Old Gear. Not saying the crafting system itself is bad, and we already have a lot of mods that allow us to craft items that should have been craftable. What I want to see though, is a method from which we can upgrade OLDER gear to be as good as new gear. Personally, I preffered my Ebony Armor over that of the Dragonbone I later came to wear, but the stats couldn't be ignored. It would be nice that when we learn a new armor, it gives us options of reinforcing our existing armor to levels similar to the highest armor we can craft. Example. I can make "Dragonbone Reinforced Ebony" which has the same ratings as Dragonbone Armor, but costs more Ebony Bars and Dragonbone. Maybe I really like that Iron Outfit, or that Leather Forsworn Outfit. Allow me to reinforce it with Dragon Scales or sections of Malachite to improve them up to those armor levels. One of the appeals of these games is the look of your character, and I don't really want to look like an evil death knight just because I want the best Heavy Armor values.
Better Storage and Organization. Mentioned this before, but I want to see storage installed in more areas around our houses, placed in logical locations. A alchemy satchel located on the alchemy table, or a nearby alchemy chest. A drawer for Soul Stones. A weapon crate for weapons. Etc... Would also like to see them utilize the organization methods of our regular inventory, so everything is not a massive pot of random items.
Adding to this, I would also like much better naming systems for some items. For instance, Potions are often all over the place. Health potions are never next to eachother, so you have to search through just to find the ones youy have. A simple change to the naming scheme could fix this so that the main part of the stat (say, "Health" or "Magicka") are at the front of the name, rather then the back. (Instead of Potion of Minor Health, it would be Health Potion (Minor)) Thankfully I heard someone is already working on such a mod.
These are just some of the things I would like to see, most of them just for convenience and to improve my playstyle, while keeping the core of the game intact.