Basically I feel that something like a sub-job system or any sort of customization is the most direct way to further the depth of the overall gameplay.

These could amount to less single abilities, such as Raise being available should you choose white mage, Lightspeed if you choose Astrologian, or Chain Stratagem should you choose Scholar. It could include passive traits, such as increased running speed if you choose Ninja, or Dualcast if you choose Red Mage. Some of these abilities are rather powerful, and many of these address many of the issues player face in choosing specific jobs. Choosing Black Mage would be less concerning during fights with lots of movement, if they only had Red Mages Dualcast. Choosing a job without any form of resurrection is less concerning when it can be made available to you regardless.