My idea:
Anytime you would learn a NEW SKILL (as in not a II or III spell), you instead have a class quest you have to do to earn those skills.

I hated scrolls in FFXI. Mages started off incredibly gimped and the RMT made it impossible for newbies wanting to start out as a mage to actually buy anything. Good luck trying to farm for a scroll when you have nothing but your basic skills.