[Esther]

I think perhaps three menus on the root battle menu is the best way to go about this:

"Class Skills," where all active skills gained by spending Skill Points in a class reside
~Hanging, Retreating Swipe, etc.

"General Skills," where all active skills gained by being a member of a certain race, by spending a Trait Point or a Subpath Point, or by equipping an item or a set bonus, reside -- ~except~ the ones that currently display on the root battle menu.
~Kick, Guard, Capture, Restrain, Banquet, Gain Air, Black Rend, Life Drain, Essence Blast, etc., but ~not~ Skip, Sub-Attack, or Maneuver: Special Attack

and "Passive Skills," where all passive skills reside, regardless of source, so that you can read the text thereof during battle.
~Sanguine Crest, Golden Eyes, Yomidori, Evasion, Stalemate, etc.

Bonus points if we can have the ability to re-arrange skills in battle, by dragging them up and down in their in-battle list.