Let it take after job-specific Bonus (Secondary) Attributes. As one does content --be they quests, instances, leves, or anything else that previously granted Materia-- they generate AP*. Each tier, the AP cap increases (e.g. 600 in the Abyssos tier, maybe 640 by next). This customization is done through job-specific plates, whereby one sets up to 5 stat goals in order, such that the last is the dump stat (e.g., 6.33% Haste if possible -> 12.5% Haste if possible -> 20% Crit if possible -> Equal Crit and DHit dump).
I.e., a customization system done in the most convenient way possible... that also happens to slightly shrink the brief, minor inertial advantage of raid gear. No Extract Materia chores.
Gil sink and crafter privilege to be made up elsewhere (e.g., by offering enhancements to the armor itself, attachable without item trades).
* (AP = Aetherial Power, per old FF
Ability Points, since Materia Points would look like Magic/Mana Points; Dynamis [Points] is likewise spoiler-y and has a not-great acronym.)