Here's my top ten, in no particuar order:
1) Make AoO and using miniatures in gaming optional again. Stick it in a sidebar where it belongs, or even in a seperate book altogether.
2) Fix grappling, natural attack / unarmed attacks so the rules are consistent and clear by making them all natural attacks, period.
3) Bring in the base classes from d20 Modern and make fighter, apprentice mage, rogue, etc occupations so we can have Smart Rogues, Tough Mages and Strong Druids. I'd like that. Bring in talent trees and make low-level spell casting access a bunch of feats with a pre-req of "must be of the right occupation". Have Druid, Cleric, Mage as Advanced Classes with standard spell progression.
4) Remove Level Adjustments and replace them with a Feat Cost. What is now +1LA will have a Feat Cost of 1, so you've no free feat at first level. +2 LA becomes Feat Cost 2 - no free feats at 1st or 3rd level. Playing powerful monsters has nothing to do with "Level" at all (Hit Dice still apply, however). That makes the more unusual monsters attractive to play without being too overbalanced. Humans still get an extra feat at 1st level; in effect, they're Feat Cost -1.
5) Ditch variable dice for weapon sizes. Make weapons "small, medium, large, etc" and say that a wielder can use a weapon one size larger than them two handed only. Anything larger is used two handed with a cumulative -4 penalty. So a halfling can wield a shortsword (which is a small weapon) just fine. A longsword (a medium weapon) is two-handed for a halfling and a greatsword (a large weapon) is two-handed and at -4 to wield. That's much better than the current "halfling greataxe" nonsense.
6) Add in penalties for hit point loss. When you lose HP = your CON, make a DC15 Fort save or be at cumulative -1 to all actions until rested and healed. You're injured, so act like it

That'll make the game much grittier and encourage tactical play instead of the PCs being invulnerable to all but the last hit.
7) Get rid of the whole CR/EL/LA fiasco. They all measure a monster's power, allbeit in slightly different ways. Make it ONE number which measures a critter's overall capabilities. Use Feat Cost (See above) as a control over it's playability as a character race.
8) Make XP a simple calculation rather than a table lookup. Have each "CR" (or whatever it's called) = 100XP and put the emphasis on GMs giving XP for good role-playing rather than dice-rolling.
9) Make a beginner's boxed set which is like the D&D Basic set to take characters through levels 1-3 with a sample dungeon, monsters, etc. Provide all the rules they need for this level of play, but no more.
10) Also provide a one-book system which gives character generation, skills, feats, some spells, some monsters and DM advice. Make it like the D&D Rules Cyclopedia - a resource for experienced players rather than a newbie book so it's text heavy, stuffed full of rules and options and a perfect "Bible" for in-game rules decisions.
EDIT: And get rid of alignment restrictions for base classes. That's a campaign-level decision, not a rules-level decision. I think that's a given now though
