The option some racial traits to be replaced with racial feats.
I miss monster/template/ racial paragon classes.
In a sourcebook like Unearthed Arcana I would offer as optional rules to can add abilities scores as Courage (hold against stress by menaces), Grace(karma/fate/luck, a enough clean soul to resist supernatural attacks or curses), Talent(dancing, playing music, handcrafting, (keys of martial) arts) and astuteness (social manipulation, noticing about little details as clues, fast mind for stressful situations) and some "sub-abilities" would work like bonus feats (perception, for example).
Distinction between the level of power (unlocking higher powers, more hit powers and bonus attack) and level of knowledge (all you have studied and remember in your memory).
The samurai, ninja, sohei, shadow assassin, swashbuckler and gladiator should be martial adepts, classes with martial maneuvers (special attacks from "Tome of Battle: Book of Nine Swords". Warden and Seeker classes as "primal martial adepts".
The totemist-shaman and favored soul could be soulmelder classes (from "Magic of Incarnum"), using soulmelds to get powers like monster traits or softer version of monster templates (feytouched, half-dragon, half-celestial).
Storytelling points as reward to "buy" special background points (allies, for example).