A D20 base system; the core works, no need to change it.
Some consolidation of the more complex parts of the game. There's no need for the multiple different types of almost identical rolls for special maneuvers like trip, disarm, etc. Every attack should either be "attack v. AC" or "opposed attack v. opposed attack." Similarly, I think some skills could be combined for a shorter list.
I'd like to see a "magic attack bonus" that increases by level, just like BAB. Even fighters and the like would get a small advancement, just like wizards and co. get small BAB advancements. The "MAB" would impact spellcasting in all the ways BAB impacts combat.
Related to the previous point, just as Strength increases attack and damage rolls, Dex increases AC, and Con increases HP, the other three stats would do the same for magic-related combat. Int would add to one's ability to damage/affect someone with magic, Wis would add to one's ability to avoid magic, and Cha would add to one's ability to resist magic.
A slightly lower baseline of magic items per level, and a higher baseline of feats/stat bumps over the course of levels.
A combat system of scalable complexity, allowing for the use of minis, or not--and complex tactics, or not--as the players choose.
A core rules set that emphasizes feel, mood, environment, and plot as much as it does combat and exploration, with all elements equally supported and just as easy to remove for those who don't want 'em.
A consolidation of concepts such as CR, LA, HD, and ECL. While I'll be the first to admit I'm not sure how to do it, I really feel like one or two of those really ought to convey the necessary info.