The idea of paying for Anima sounds nice. And it could actually work. Or perhaps the quest idea, as long as the actually quest requires some time or skill to complete.

But! Any way of recovering Anima (apart from the waiting..) should be disabled once other methods of transportation become available. I think Anima should be used only in emergencies or when time is low, and of course airships, mounts, walking, etc.. the main method. So, with those implemeted people should not have any issues with Anima managment.