I've been thinking along these lines and have a broad idea on how to go about doing it (but have no details yet!)
Extract each item of a character, so HD, casting levels, skills, save bonuses, BAB etc. Assign an XP value to them. As charcaters advance they use their xp to buy advances in what they want.
So lets for argument sake say that a BAB +1 costs 100xp, caster level 1 costs 100xp, d4 hp costs 25 xp, d6 hp costs 50xp, d8 75xp, d10 100xp, d12 125 xp, d4 + d4 80, each starting skill 50 xp, each starting feat 100xp. A character starts with 500 xp- he now spends those for his starting package and spends xp gained as he advances in level to purchase additional skills/skill advances, etc. Under this system you could theoretically have that wizard tossing meteor swarms with only 1d4 hp, or maybe with 20d12 hp, BAB +20 and caster level 18!
Ok, it needs a lot of wor (and how to calculate the raising increases for HD, caster levels, feats etc so that at a similar xp spend to normal d20 the characters are comparable, but under this far more customised to the players vision without the need for prestige classes!)