I like the idea that each job has its own Job Level and each Level grants you a new Passive Trait which enhances a core value of the Job itself.
Job Points for Job Levels should be earned by doing things like Questing, Partying, Leves, Companies. While Weapon Class Skill Levels should be earned by straight up combat as well as Leves and Partying.
Your actual stats could be established Four Ways Excluding Armor.
1. Your Weapon Class Skill Level
2. Your Job Level
3. Stats granted from skills equipped. Equip skills from your current Job and Class and you get more stats then if you equipped them cross class.
4. A Mix of two or more of 1-3.
Output of damage/healing power would be based on your Weapon Class skill level while your bonuses would be given based on your Job Level. The higher your Job level the more bonus passive traits you have so you become more powerful.
A White Mage Job Level 1 Might get +5% Healing Potency and the Skill: Benediction to Equip.
While a White Mage Job level 10 would have +15% Healing Potency, +10% MP, +5% HP, Trait: Auto-Regen, Skill: Benediction, Spell: Holy, Spell: Bar-Element, Spell: Flash.
These Bonuses, Traits, Skills, and Spells would be White Mage Only because they define White Mages. While Cures from your Conjurer are cross class.
Just more ideas.