The last letter from the producer listed the job system as something that was being worked on separately from the armory system, so while that doesn't guarantee anything, hopefully they'll be working something out similar to this.

If the advanced jobs are going to "grow out" of the standard jobs though, then I think your standard jobs should be more generic, something like: Mage, Fighter, Rogue/Vagabond. When you progress to White Mage, you can still use your shared Mage abilites, but start gaining unique White Mage only abilites. Black Mage can also use those generic Mage abilities, but gains unique Black Mage only abilities, etc.

Cairdeas, myself, and others have a pretty long thread going on about this basic idea (job system alongside armory system), if you haven't checked it out already, please do:

http://forum.square-enix.com/ffxiv/t...pecializations