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Yeah, can you not equip a job crystal and then use a lot more cross class abilities? Im pretty sure you can use every ability you have learned on another class without a job crystal equipped. The tradeoff for the job crystal is specialized abilities.
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Keep in mind that soul crystals don't even necessarily have to be involved, they can easily make it so the quest to unlock the job has the job unlock quests as perquisite to starting them.
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Have it work like the summoner does for Conj. Have it evolve skills. Savage blade can evolve into a higher damage or a ultity skill that drains life or mana like it did in FFXI.