I think...

...the best thing for them to do is allow you to equip a job and gain bonuses to classes that fall under that job type (EX: Warrior = Gladiator and Marauder get bonuses, Monk = Pugilists get bonuses, Dragoon = Lancer gets bonuses, Archer = ...Archer, White Mage = Support Spells get bonuses, Black Mage = Damage Spells get bonuses, Red Mage = half of the Black/White Mage bonuses, etc).

Or something along those lines, so that you still have the freedom of the armory system with the ability to define a role for yourself.