I feel like the two ways sub-jobs might work here could be as variations on specialisation/talents with jobs that aren't actually playable.

The more typical specialisations, where like... a Summoner could pick "Evoker" which might focus on strengthening their Summons or "Invoker" which enhances your stuff.
This could even change stuff about the class, like smn subjobs might get different summons, a nin could get a different mudra.

The other is where your sub-job can be picked from a group available to various classes.
So maybe, "Time Mage" might be available to the DoM jobs and has features like faster casting and suspending timers (freeze enochian/af, dwt, etc) where "Green Mage" might focus on enhancing buffs/debuffs.
Ideally, the sub-jobs would be set up so they're a meaningful choice, maybe one is more of a greedy dps option, another might open up new options for a class. Like a Tanks might have a sub-job that's really the tank sub-job while there's also a more off-tank/dps option.