Perhaps each of the job stones should give an effect that aids each of the jobs and helps to pigeon hole them even further.

Ex. Paladin: When equipped with the Paladin Job stone, Blocking an attack restores a small amount of MP.
Dragoon: When equipped with the Dragoon Job stone, missing an attack increases the critical chance of the next WS.
Monk: "" Monk "", evading an attack increases attack power for a limited time.

etc. Just something outside of skills and AF to make the jobs more appealing and helps to negate their short comings, making them a more viable option than their class counter parts.