I'd like the BAB for feats instead of HD thing more if it wouldn't screw Monks, Rogues, and Soulknifes. Plus, there are various effects that alter BAB... what does a Cleric with Persistant Divine Power do? It's up all day long...
Slowing casting rate for the "I get to cast everything" guys seems to work. After all, the Factotum's not too bad. Even just making it so you gained a new spell level every 3 levels instead of every two would work (so you hit 2nd level spells at level 6). The Sorcerer could maybe still have his normal cast rate, so Wizards, Clerics, Druids, and Archivists would be slow but have bredth, while Sorcerers and Favored Souls would have depth in their areas. Healers... we'll just give them the full casting, okay?
Of course, there's something to be said for simply saying "screw it, make your characters with T3 and T4 classes only. Done." It's not like there's any character archetype missing if you do that. The "call upon the powers of the gods" guy is the Crusader, though.
JaronK