I have had it in mind for a long, long time to turn the d20 class based system into a far more skill oriented one.  I have had a fair bit of experience with the West End Games d6 model, with the WoD d10 model, and the 7th Sea R+K model, and will most likely be borrowing concepts from them liberally.

STATEMENT OF PURPOSE:

I propose the beginnings of a new system, oriented towards enabling more free-form character advancement and less of a tiered system of plateaus that the current 20 level system encourages.  I propose a system that rewards magic but makes it difficult to attain, that enables any and all to become "casters" who dabble in magic, that lets non-magical folks shine in whichever arenas they wish, and that easilly accomodates all manner of character archetypes and ideas.  I propose a system that uses the allmighty d20 in conjunction with skills and stats to resolve almost all conflicts, with perhaps a bit of the feats mechanic kept in for variety.

With that said, let's fire away!

STEP 1: REVERSE ENGINEER D20

D20 is based around a few simple concepts: a d20 is used for almost every roll, high is universally good, low is universally bad.  This is a great starting point.  I'll keep it.

D20 is based around several independent but quasi-interlinking mechanical areas: combat (initiative, bab, and AC), passive defenses (saving throws, hp, and AC again), and non-combat know-how (skills) and miscellaneous abilities (feats, racial and class features) which can fall into any of the other categories.  I like some of this, so I'll keep that which appeals to me most: distinctive racial charicteristics and the concept of feats.  Class features will either disappear into skills or become quasi-feats.

D20 favors offense over defense in combat, almost unconditionally.  Given the choice between a defensive action (healing, fighting defensively, casting a defensive spell) or offensive action (attacking, casting offensive spells, disrupting enemy actions), the offensive action is the better choice 90% of the time.  I dislike this aspect of the game, but understand the reasons why this decision was made.  Offense, as an active form of play, is more rewarding than defense, a reactive form of play.  I will have to consider this.

D20 overwhelmingly favors spellcasting over all other things.  Each spell is a unique rule unto itself, and the ever-expanding number of spells means spellcasters become increasingly more powerful as their options, and thus gameplay power, become increasingly larger.  I dislike this aspect of D20, and if possible will attempt to diminish it.

I feel these are the bare bones of the system.  There may be other aspects I'm ignoring or have glossed over, but I think those are small potatoes compared to the bigger picture of die rolling and mechanics.  You can build whatever game you want out of the superstructure of the D20 superhero-esque mechanical base.

STEP 2: LISTS!

Here is a list of all the skills in the D20 SRD, including the XPH:

Appraise
Autohypnosis
Balance
Bluff
Climb
Concentration
Craft
Decipher Script
Diplomacy
Disable Device
Disguise
Escape Artist
Forgery
Gather Information
Handle Animal
Heal
Hide
Intimidate
Jump
Knowledge
Listen
Move Silently
Open Lock
Perform
Profession
Psicraft
Ride
Search
Sense Motive
Sleight Of Hand
Speak Language
Spellcraft
Spot
Survival
Swim
Tumble
Use Magic Device
Use Psionic Device
Use Rope

Of those skills, there are many that can be compressed into one skill.  For example, Autohypnosis can be compressed into Concentration.  Here is a revised skill list with the compressions I think should be made:

Acrobatics (includes Balance, Escape Artist, Jump, and Tumble)
Athletics (includes Climb, Ride, and Swim)
Alertness (includes Listen, Spot, and Search)
Concentration (includes Autohypnosis)
Craft
Disable Device (includes Open Locks)
Charm (includes Bluff, Disguise, Handle Animal, and Perform)
Knowledge (includes Heal and Survival)
Linguistics (includes Speak Language and Decipher Script)
Manipulation (includes Diplomacy, Intimidate, and Sense Motive)
Sleight Of Hand (includes Use Rope and Forgery)
Sneak (includes Hide and Move Silently)
Spellcraft (includes Psicraft)
Streetwise (includes Appraise, Gather Information and Knowledge: Local)
Use Magic Device (includes Use Psionic Device)

The second list may be going overboard, but already the 39 (more, if you include all the varieties of Craft, Profession, Perform, and Knowledge) skills have been narrowed down to 15.  This may be going a bit too far but it's easy to expand skills.

Now let's add in the "skills" in D20 that aren't dependent on skill ranks:

Melee Attack rolls
Ranged Attack rolls
AC
Initiative
Endurance (mainly a function of Con)
Weight Lifting (mainly a function of Str)
Movement (mainly a function of race)
Passive Defenses (saving throws)
HP (mainly a function of Con and class)

Some of these make sense to add.  So let's add, at the very base, a few varieties of combat skills:

Melee (hand to hand fighting with a weapon)
Ranged (ranged fighting with a projectile weapon)
Brawl (hand to hand fighting without a weapon)
Dodge (getting the fuck out of the way!)
Parry (blocking with a weapon)
Toughness (takin' a lickin' and keepin' tickin')

Some of these may stay, some may go, but I like the basic idea of 3 combat skills, 3 defensive skills.  Maybe Parry can't be used against range, and Dodge against melee.  We can think this out more later.

Stealing a page from the various d6 or d10 books I've amassed, let's group these skills under stats.  Maybe your ranks in a skill plus your stat mod add together to be the number you add to a d20.  Let's try to extrapolate the list I made earlier and match some of those skills up to stats.  I'll list STAT, Skill (specialty), in that order

STRENGTH SKILLS:
Brawl (specific manuever)
Melee (specific weapon)
Climb (face climbed? maybe none.)
Jump (can't really think of any...)
Parry

DEXTERITY SKILLS:
Acrobatics (balance, tumbling, swinging)
Dodge (none)
Ranged (specific weapon)
Ride (specific animal)
Stealth (move silently, hiding)
Sleight of Hand

CONSTITUTION SKILLS:
Endurance (type of activity)
Movement
Lifting
Concentration (circumstances)
Fortitude
Swim

INTELLIGENCE SKILLS:
Craft (type of craft)
Knowledge (type)
Healing
Linguistics (language)
Disable Device

WISDOM SKILLS:
Alertness
Gambling
Manipulation
Streetwise

CHARISMA SKILLS:
Charm
Perform
Artistry
Use Magic Device
Willpower

This is a basic list... now some more things are starting to take shape.  I'm seeing a basic framework of Skill Mod + Skill + D20 for resolution.  Initiative can be an awareness check. Fort/ref/will saves can be fortitude, acrobatics/dodge, and willpower skill checks.  AC can be dodge or parry.  Movement and lifting can be determined by the relevent skills.  This is a base framework, I'll probably flesh it out more soon.