As I've said before, the best way to do this would be having the normal, non-quested spells be learned naturally, but tying them to a sort of hunting log.

An idea I had for this was that story-wise, a BLU sort of knows these spells from monster observation, but needs to kill and absorb a monster's essence in order to get a true understanding of a spell. So if you learned, say, Acid Mist at lv10, you'd have a hunting log-type entry that requires you to kill 3 Ochu type mobs to unlock Acid Mist's full power.

The big spells would be learned via the job questlines, and by design each quest would involve the monster you'd learn the spell from (so if the lv35 quest rewards you with Bad Breath, that quest is going to involve a marlboro type mob).