Omg !
The more I read this, the more I am tempted to throw all 3e/3.5 books in a box and dedicate my time to AD&D instead...
Paladins need empowering to be rebalanced: it has to do with the number of key abilities required for the class to work... Str, AND Wis, AND Cha, AND preferably Con and Dex makes for a tough balancing act. The old 1e "spellcasting as a Cleric two levels lower" was good.
Most semi spellcaster's casting levels make them particularly good at shining shoes: they're good at utility spells, but they become useless fro offensive purposes.
The fact that the golf club effect was not mentioned means people like it? Adamant-iron-silver-magic-good-axiomatic-cardboard-papercut-fruitiness? "DR 15 still applies 'cause your weap didn't have bubble-gum"
Facing is good. Flying maneuvers w/o facing sucks. I like to know that the dragon can sit on me, but not breathe nastiness at me... And no, facing does not necessarily call for minis.
Useless lower level spells when climbing in level... That's a bad rule.
The Touch AC is fine... We house ruled it that way in 1e, 2e, 3e vindicated us, and usually, a save will apply (except a very few exceptions) once the magical attack touches.
Bards need a boost... Sure they can make decent buffers, but they are at a disadvantage in most adventuring environments.
Multiclassing works, but should be limited to perhaps three classes, including the final PrC.
Gestalt is best.
Bad epic system.
Bad D&D power curve.
Bad absence of alternate life experience mechanics allowing NPCs to progress as alchemists or wizards while playing in the lab or the library.
So many things to fix...