Weapons & Armour
Minor: I would bring back longswords, set them up as before (higher damage, slower, better reach compared to shortswords).
Minor: I would bring back durability but keep Smithing improvements; you would be able to smith things to make them more durable aswell as more damaging (maybe even turn long swords into shortswords at higher levels, something like that).
Major: Change the basics of the system, so that materials work in different ways, as opposed to just steadily being better as the game progresses (see below).
Example material system:

• Iron- very basic weapons
  
• Steel- superior to iron, slightly heavier
  
• Dwarven- superior to steel, heavier, swings slower, makes for better with blunt weapons
  
• Orcish- superior to steel, heavier, swings slower, makes for better with edged weapons
  
• Ebony- superior to steel, lighter, can take stronger enchantments, much rarer and expensive

Armour could work similarly; some materials making heavier armours, some being better for enchanting etc.
These are just examples off the top of my head but that's how I'd like it to work; I think it would be more interesting than just grinding away til you find better and better armours; that said Skyrim has gone some way to improving that via Smithing.



Alchemy:
Minor: Bring back the mortar and pestle, but only that, so that potions can still be created in the wild. As a trade off, these could be weaker than potions made by the alchemy stations.



Crossbows:
Major: I would love to see crossbows added in. I don't think this would be difficult, as each game tends to leap forward in time many years and crossbows aren't really beyond the technological level of the people in the Elder Scrolls series.
A few basic types could be:

• Common Xbow- single shot, average reload, damage, etc
  
• Hunting Xbow: single shot, highly accurate, long reload.
  
• Shielded Xbow: equipped bit a small shield at the front, provides a small amount of armour rating, can be used to pistol-whip (crossbow-whip? lol)
  
• Spring-loaded Xbow: utilises a clip, can fire multiple shots before reloading, possibly of Dwemer origin? (let's face it, they probably could make something similar)

I think it would be good to see this implemented as another skill, alongside Archery. Could be called Marksman again?
Each crossbow could use different ammunition (Hunting Xbow- long bolts, Spring-loaded Xbow- darts etc)
A method of using the crossbow along with a shield would be interesting aswell, but probably unlikely as reloading would be pretty impossible. They could be used by the guards that patrol some of the richer cities, whereas smaller settlements still use bows. I would definitely keep bows though, obviously.



Lockpicking/Security/Containers/Loot:
Major: I would bring back the old (Oblivion) lockpicking minigame, but use it for specific areas. Possibly use the old one for doors and the Fallout-style one for chests?
Minor: I would like to see different lockpicks, maybe just another type that lasts longer (I'm not good at lockpicking and don't want to have to track down the Skeleton Key every game -.-)
Minor: Every container has an animation when opened or closed.
Minor: Chests never contain clutter items. Just doesn't make sense to me.



Speech/Interaction with NPCs/Marriage:
Minor: I'd like to see the effects of conversation a lot more ingame, with more varied options to take good/neutral/evil routes, and lasting repercussions of each. Persuade/Intimidate was a nice addition but I think it could have been implemented better. Maybe some characters flee when intimidated, or turn hostile? Being an evil character should reflect more as you play. Maybe you kill half a town and the shops refuse to sell you? Extreme example but it makes my point :s
Minor: Marriage should not happen because you brought someone a mammoth tusk. Maybe bringing a sword back from Mzinchaleft (only for her never to use it again ffs).



Racial Abilites:
Minor: I'd like to see the differences between each race much more emphasised: Nords are stronger, Khajiit are stealthier etc.



Perks & Character Development:
Major: I would implement three sets of perks:

• Racial Perks: For example; Nords get stronger and can carry more weight, Imperials get more speech options, Khajiit can use Nighteye for longer etc.
  
• Generic Perks: Every 2 or 3 levels, similar to the Fallout ones really: fast travel when over-encumbered (this could maybe be a racial perk for Nords and Orcs), basically any perks that would be useful for any type of character.
  
• Skill Perks: I actually like this system as is. Maybe fiddle with it so it acts like less of a 'tree' and you don't need certain perks to learn others (for example, in the skill Two Handed, requiring Champon's Stance to learn Great Critical Charge).

It's a lot of work but again I think it would add a lot of depth to character development.
Major: I would bring back birthsigns and attributes. Maybe not use racial perks but just bring back attributes, now that I think about it.



Plotlines:
I would like to see good, neutral, and evil endings, but am aware this will probably never happen as it would probably mess up lore etc.



Items:
Minor: Bring back labelled potions, and add labelling for soul gems.



Spells:
Minor: Keep the current system, but bring back spell customisation, that was fun.