Well they answered this, it's mainly because it would be a huge undertaking to program the systems to let you change your appearance and pay for it.

Fujito: As part of FFXI’s policy, there has been something in place from the beginning of the game where we wanted players to keep their name and appearance. Also this is not easy to implement from a system perspective, and as such we do not have any plans to add a service that would allow you to change your character’s appearance.