This is an idea I thought about while questing in Empyrea but what if our Wizard was 'evil' for an Arc? Now I say 'evil' cause of course it wouldn't be willingly. Maybe have 4 main villains that we 'work' with while having to fight the good guys trying to save the Wizard (Bat, Mellori, etc.). The end can have you returning to the good side and fighting the 4 villains.
That's really all I have for it cause haven't really thought it out but feel free to add to it or any ideas you can think of for future arcs.