I'd throw a lot more thing sinto the skills mechanic. Combat, spells etc. I'd make certain feats the way you gained access to special skills, sort of like the force skills work in star wars.
I take force sensitive, i get access to 3 or 4 skills, and access to more advanced force feats, I take control I can now take the control skills. But in D&D it would be I take divine magic primer and I gain access to knowlege religion, spell craft, scrying, and knowlede religion, it also gives access to the feats spellcasting(cures) Which gives you access to the skills cure HP, cure disease, cure poison, remove cure etc.
As you put more ranks into eack skill you would learn more spells and spels would be mroe effective,(higher DC to resist, penetrate SR better etc.) You classes would give access to these feats at a certain rate , and you could take diversify with your standard feats. This would apply to fighting skills as well, the fighter might start with the feat, beat people to death up close, kill at a distance. These would give access to fairly broad skills like slashing weapons, blunt weapons etc. The more ranks the higher ACs you hit, and also special tricks would be learned. Improved disarm wouldn't be a feat anymore it would now be a trick you could pick up after you have 5 ranks in slashing weapons. There would be more advanced fighting feats that let give access to special skills that take you fighting to a supernatural level(also allowing you to combine tricks you learned unde blunt with slashing weapons) reducing the need for tons of items on all characters.