There are a few things I think could be done better, if not simpler.
The first would have to be damage bonuses as compared to increased dice, as mentioned. I believe the Monster Manual has a chart for damage progression, and I use that when at all possible. However, there are no rules for converting bonuses into bonus die size... and the system still doesn't always scale well.
Then there's percentage chances. No matter your level, an opponent hiding in total concealment will be protected against fully 50% of attacks. Consider this: An invisible ogre is attacking the party. Krusk swings his greataxe at the square with the ogre in it, at a height roughly congruous with ogre thighs. He's fought invisible opponents before, and is intimately familiar with the gait of ogres; he shouldn't even need to look to be able to hit the brute (AC 8 to touch). Yet for all that, he's got a 50% miss chance right off the bat (Unless he's got blind-fight which . And then there are arcane spell failure checks in armour, which can foil even the most experienced caster. I know, they can take feats to offset some aspects of armour, but they still have the failure chance. Is there no way to abrogate this?
I'd personally suggest a more unified mechanic to replace those percentile rules; perhaps just use the AC bonuses from cover to reflect concealment protection (and use +13AC for total concealment). As for spellcasters, have a DC for casting somatic spells in armour; make a Spellcraft check (using Dex as your skill modifier) against a DC equal to 10+(%failurechance/2.5)+spell level or something like that.
Not that I'm actually doing this in my campaign, but it seems sensible to have a truly unified mechanic. That's what I'd do with my own system.