Well the idea would be that could be a possibility (depending on what type of special "materia") they allowed us to meld into the job crystal. The sad thing is, right now SE over simplifies how jobs work in this game and essentially don't give us choice in cross class skills or stat allocation. What I mean to say is, even though those are there people are "forced" to choose specific ones. Not saying this wouldn't happen for this system, but at least the choice could be harder.
I.E.
For Jobs:
Extend the duration of GL3 when using X-Skill by 2-3seconds or increase potency of X-skill. Maybe make it so you can't have both lol.
or
Augmentation: Inner Beast's wrath stack consumption is lowered by 1. (You can use up to 2 of these augmentations.)
For Class:
Increase Vit by 5 and Parry by 10. (This would be a newer special "materia") for the soul crystal only.
Increase Str by 5 and Skill Speed by 15.
Increase Dex by 5 and Crit by 10.
Increase Pie by 5 and Spell Speed by 15.
Increase Mnd by 5 and Det by 6.
Increase Int by 5 and Crit by 10.
Something along those lines.