No more 1.5x Str bonus with a two handed weapon. Make this a feat, to even it out with two-weapon combat. My idea breakdown would be.
Power Grip
Str 13+
You gain 1.5x your strength damage to damage when wielding a non-light melee weapon in two hands. You may subtract up to -5 from your attack bonus and add the same amount to damage (with a light weapon you only add 1/2 this bonus to damage).
Normal: You add your strengh bonus to melee damage.
Power Attack
Str 15+, BAB +6
You can subtract up to your base attack bonus to hit and add this amount to damage. When wielding a two handed weapon you instead add double this armount to damage.
Two-Weapon Fighting
Dex 13+
You reduce the penelity to hit for fighting with two weapons by 2 points. You are also considered to have no off-hand, removing the standard -4 penelity to hit and with an off-hand weapon.
Improved Two-Weapon Fighting
Dex 15+, BAB +5
You can make a second off-hand attack at -5 to hit
Special: If you have a BAB of at least +11 you can also make a third off-hand attack at -10 to hit.
This solves a lot of the power disparity problems with Two-Weapon fighting vs. A huge sword and makes fighters better fighters (you can't just make an 18 Str cleric of Kord and be good with the greatsword). And while the ideal power attack-damage ratio is 1 - 1.5 at the cost of two feats 1-2 should be closer to fair (and 1-1 for a light weapon should likewise not be so bad, given that it would take 4 feats to really make it work).
More unified weapon rules.
The only real difference between most simple and martial weapons is the crit factor. A mace is basicly a longsword that dosn't threaten a critical on a 19. Why not just give them identical stats and make it so if you have simple weapon prof. you have a 20x2 crit and with martial you get a 19-20x2. So your cleric can use a sword, but not as well as a fighter.
Better multi-classing rules.
This covers better balance across all levels (less front-loading), no XP hit and the stupuid number of prestige classes (which are 'needed') as well as non prestige-class rules to fix multiclass casters. Multiclassing is the best rule change in 3rd edition, but there's still a lot of rough corners to smoothe out.
More consistant core classes.
Base the mage, fighter and cleric off the 3.x rogue. Rogue is the perfect class in 3E, you can make all sorts of archtypes with it, you get useful abilities at least every other level and there's an incentive to stay with it all the way (special rogue only abilities) or to dabble in it a bit. All classes should be built like this. The more exotic once can be more different, but the big 4 should all have some symmetry.
Give the fighter unique special abilities at 10th, 13th, 16th & 19th, and some extra defense abilities at 3rd, 5th and 7th.
Mages and clerics mirror sneak attack advancment with new spell levels. So smooth them out with some bonus feats from a list and unique abilities at 10+ just like the proposed fighter and 3e rogue.