Even Yoshi-P has said he's not fond of the job/soul crystal system. It's a weird relic of 1.0. Unfortunately, getting rid of it would require rewriting a lot of job quests (several of them, including black mage and dark knight, explicitly use the soul crystals as a plot device), and redoing how summoner and scholar split off the same class. It's just one of those things they want to work on but can't prioritize over new content.