It's not going to be complicated. It'll work exactly how it does now except that the class/job division won't exist.
For example, if Dragoon was a new job, instead of leveling Lancer and plugging in the job stone to become a Dragoon you just start as Dragoon and level Dragoon.

The whole class/job thing is little more than an issue of nomenclature and some superficial differences. Mechanically it's not like there's some fundamental difference between class and job that makes this complex. You trade cross class skills for more specialized skills and some stats and get a new logo.

I would not be surprised if you still get a job stone. It'd function the same way. Adds some stats and allows you access to the "job" skills (ones taught by the trainer) and limits you to 5 cross-class.