If the class-based system is to remain (and I have no doubt that it will), I'd like to see the reinforcement of archetypes that those classes represent.
The Barbarian is fine. The only change I'd make is to rename the class to Berserker instead. Sure, they could switch some abilities around, but nothing major is needed, because the class works.
The Bard got better with 3.5E, but it's still not clear that the class represents a "jack of all trades" archetype. I'd increase the HD to d8, remove all alignment restrictions, and find some way to allow bards to mimic other class abilities (similar, but not the same, as the recently presented chameleon prestige class).
The Cleric needs to loose Heavy Armor Proficiency. As far as spells go, I'd like to see both clerics and wizards utilize a system similar to AU. To stay in line with their current abilities, cure/inflict spells would always be considered "prepared."
The Druid archetype needs to be reinforced by adding the wildshape ability from 1st level. To balance it out, each druid would have a limited list of shapes he can turn into. Also, the druid should probably be a spontaneous caster with a limited list of spells known (excluding all summon nature's ally spells, which they'd get for free).
Nothing wrong with the Fighter other than the lack of high-level feats. There should be a feat chain that allows a fighter to be as good in unarmed combat as a monk (if not better).
Monks need to loose the unnecessary alignment and multiclassinjg restrictions.
Paladin. Ugh. Although my first impulse is to drop the class altogether and make it a PrC (as I have done IMC), I understand that many people like the archetype and think it is fit for a base class. Rename it to Champion, and allow Champions of different alignments, with slightly different abilities and flavor.
The Ranger is currently not a master of wilderness combat, which is what he should be. Something needs to be done, perhaps along the lines of incorporating some Complete Adventurer Scout abilities into the ranger class (such as the bonus to AC when on the move). Spontaneous spellcasting (as druids).
The Rogue is fine as a master of skills and stealth.
Sorcerer is the most controversial class of 3.x. To divorce it even further from the wizard, I'd take the Complete Arcane Warlock, drop the alignment restrictions, and rename it sorcerer.
Wizard: see cleric.