I have a few quick suggestions, and I think I'll post them in a separate house rules thread in more detail.
1. Wounds. To combat the complaints about unrealistic chumba-wumba-iness of PCs, we change the HP system to include a simple wound system, providing a rules-based division between 'minor scrapes' which heal fast, and 'actual wounds' which you need a few days' rest to get over.
2. Combat vs. Non-combat Roles. I like Firelance's idea.
3. Ramp Up During Combat. I draw a comparison to the 'super move' meters in some fighting games. I'd generally prefer for people to pull out the big guns later in a fight, instead of playing rocket tag, so I'd work in a switch from "at-will, encounter, daily" to "standard, fierce, super" (better terminology pending). You would get access to stronger attacks as the fight went on, through a variety of methods.
If you're familiar with Capcom vs. SNK's 'groove' system, wherein you can choose six different styles for how your 'super meter' works, that's sorta what I have in mind. Warrior style would ramp up as you hit stuff. Skulk style would ramp up whenever you strike unaware foes. Flashy style would ramp up as you move around and chain acrobatic combat tricks. Various types of magic might require you to concentrate to draw mana (think Magic: the Gathering), or could grow stronger based on if conditions match your god's domains, or might improve as you sacrifice your fallen foes to an extraplanar lord.
Utility powers I'd probably leave alone.
4. Grappling. A few tweaks to the grab rules to allow pinning and stuff.
5. Skill Challenges. Use the Obsidian skill challenge rules, as devised on these boards. They're much better.