Given how the game works right now, where your stats come from your gear and players have a separate gear set for each of their jobs (with different materia at least), I don't see how "balance" is still a problem. The only truly unique thing is your job's soul gem.

I could see this being a common player objection, "I want to be a Green Mage, but I don't want to Marauder not even for a mere 30 levels". The easiest way to avoid that is to make "Green Mage" just another job like Samurai, Machinist, Dancer, etc... that anyone can switch to.