I've had trouble with sorcs and wizards being wimpy - and by wimpy I mean they usually have weak defensive spells, or they have all-or-nothing spells (often overpowered, such as greater invisibility or campaign-killing).
I would love to see a scaling mage armor spell, for instance.
Clerics are kind of odd... I wouldn't be too upset if they lost armor proficiencies, but then you'd have to give them defensive spells to compensate. However, I do not want to go back to a "sphere" system - the spheres weren't balanced with each other (and they were bigger than domains, so any balance problems with them just got multiplied) and they made clerics too similar to each other, IMO.
Magic Item Dependency
I've got several problems with this.
For starters, the GM has to hand out massive treasure hoards. (Otherwise the players get weaker and end up dying.)
NPCs are weaker because they must have less treasure. (Otherwise the players get too much gear and power.) As a result, they're not worth their CR - which is annoying when the main villain of your campaign is a high-level fighter or cleric or something. Furthermore, fighter items are more powerful and more "required" than spellcaster items, so fighter NPCs suffer doubly (or triply) because of this - they end up with much lower damage, usually, than an equal level PC fighter.
Characters can't learn to dodge. (D20 Modern, Star Wars and some other D20 settings solved this problem with a class bonus to Defense. I vastly prefer this to using only magic items and Dex to boost your AC.)
No, really, I hate having to "get your +1 ring of protection by x level or your AC sucks" whatever other "required" items there are.
This makes it really hard to design NPCs, too, or players at a level higher than 3 or so. A D20 Modern NPC (even if played in a medieval setting) is a lot easier to design. He's got his sword, his armor, maybe his shield, and maybe a bow. That's it. He doesn't need his ring of proteciton because he was taught to parry and dodge. You don't have to sit down and figure out how much gear he should have and then spend the extras, and when you have cash left over you have to frantically spend cash to boost his Will saves or AC score or what not...
And last, but not least, I hate skill-boosting items (or items that replace skill checks). You have your own character abilities, so use them.