You know, thinking about it....
Here's how I'd do the classes.
***WARRIOR***
As written, although I'd factor in a damage bonus similar to power attack into his stats. Or, keeping with feats, you could set up multiple "fighter options".
Option #1 - Damage
Every odd level, the fighter's damage increases by 1. (the fighter would be improving his attack with weapon focus, anyways, so this is okay...)
Option #2 - Attack
Every odd level, the fighter's attack bonus increased by 1.
Option #3 - Defense
Every odd level, the fighter's AC bonus improves by +1.
(note - these aren't hard and solid, or anything... just ideas)
***ROGUE***
The rogue receives an additional skill group of his choice (either Mind, Physical, or Communication).
If the rogue makes a sneak attack (an attack against a target that is already engaged in melee combat or is unaware of the rogue's presence) against a target, he can add his subterfuge rating to the damage.
If a rogue makes a saving throw to avoid damage, than if he succeeds, he takes no damage, instead of half damage.
***WIZARD***
A wizard can cast a number of spells per encounter equal to his MIND rating. Note that level isn't a factor - a wizard with a MIND of 5 can cast 5 first level spells, 5 2nd level spells, two 1st level spells and 3 2nd level spels - whatever.
As an option, a wizard can only cast two spells per encounter that are of her highest spell level - thus, a 1st level wizard can only cast 2 first level spells each encounter.
***CLERIC***
Same spellcasting rules as for Wizard, including the Mind prerequisite (thus, clerics can cast fewer spells per encounter). This will even up the spellcasting variability (wizards are better casters than clerics, I'd say). To even up the "clerics can fully heal the group in between encounters because there's no limit to spells per day", I'd suggest some sort of heal limit... or I'd just throw in reserve points (from UA) and get rid of heal spells altogether. Plus, it's simpler!