There is some modification of skills already within the game. With SMN, once you complete the quests to summon Titan and Gardua, using the skills Summon 1 & 2 is altered to no longer summon Emerald or Topaz Carby, but the appropriate egi instead.

Also, using those same skills with a SCH Soul Crystal equipped will call Eos or Selene instead of Carby.

So one need look no further than that to see how this could be implemented with future jobs.