Iv been playing through The elder scrolls daggerfall and morrowind lately and have been trying to build the perfect reformation of the leveling system. Skyrim was terrible as an RPG effectively gutting and hobbling the robust system of previous games. It removed attributes, removed and combined skills to an absurd level, removed fan favorite weapon and magic skills, and gimped the fuck out of magic.
First things first, all weapons that have been in previous titles are in with appropriately grouped skills dedicated to them. Shurikens and darts could be grouped into a throwing skill, spears and pikes in a skill etc. Spellcrafting is to be like Daggerfall, with the ability to add effects from any school into the mix, with the only limit being skill, money, and magicka costs. Design would focus on fair balance and progression instead of preventing or nerfing exploits. Thats one of the things I have always hated about bethesda is how extreamly reflexive and overkilling they are when it comes to exploits. Role playing should always be focused on player choice, which anyone familure with D&D could tell you. A DM that is super anal about strict rules and linear story telling is just about one of the worst RPG experiences ever. If a player wants to craft 1000 iron daggers to level smithing up your response should not be to nerf smithing to the point extreme grinding is required for progress.
Now on to leveling. Attributes are back, Daggerfalls character creation is used here including background generation and reputation. You not only get to choose what your character is good at, getting a head start on certain stats and skills allowing you to start playing a role immediately. A thief should be able to thieve from the start, an axe wielding beserker should be bathing in the blood of many mud crabs from the word go. Level 20 should not be the entry level for ones role or class. Skills still level up to 100, each skill level tied to overall level advancement, and also tied to a primary attribute. Level up a strength based skill, get a point of strength on level up. Every 10 skill level ups of major skills is a level up, with all other skills counting as half a major. So 10 major skill advancements is a level up, or 20 minor skill advancement. At level up you get to choose a general perk at every even level. These perks are general perks mostly affecting attributes and core character features such as disease resistance etc.
Skills on the other hand will work similer to how they worked in morrowind/oblivion, awarding perks at every increment of 25. So at level 25 of critical hitting (a returning daggerfall skill) crits will have a chance to daze a target, or each 25 levels of back stabbing increases the sneak attack multiplier that starts at x2 and at 100 would be x6 applying to one handed melee weapons, ranged weapons, and throwing weapons. Further more at 100 you start gaining master levels in a skill. Each skill has 10 mastery levels with each level of mastery granting a perk specific to that skill. For back stabbing you could get added bleeding damage with one handed bladed weapons, or a chance to render targets unconscious with a sneak attack from a blunt weapon. Further more master levels count double for main level progress so each mastery level will add 2 xp tics towards over all level progression.
Also fatigue will return, and you will once again be able to render npc's KO. Unarmed will be overhauled as a skill as well. Rather than requiring you to drain all of an opponents fatigue to damage them, you will deal damage split between fatigue and health. For example your over all hth damage could be 10, but opponents at 75%+ fatigue will take 8 pts fatigue damage and 2 pts health damage, with half fatigue damage also going to magicka. This would all also be affected by the hth skill as well as mastery perks. Also beast races would have more leathal hth damage.
Speaking of beast races, they will be slimier to thier morrowind/daggerfall incarnations, being much more pronounced as beast. Also each race would have more variations available. In the lore the Khajiit for instance have many different breeds, with some being much more cat than man, and vice versa.
This is just my first brainstorm on this, feel free to jump in and add to it.