Since everyone throw their ideas out there I'll give mine a shot.

Have a separate defensive materia slot, you can only use Elemental Resistance Materia in these. Mutamix can remove the materia you slot there separately from the other materia, you obviously lose that materia.
Add Savage Primals: Savage Garuda, Savage Ifrit, Savage Shiva, yadda yadda yadda... Make Elemental Resistance Materia relevant (not strictly necessary) to this content, bam.

If anyone else has any other idea for this waste of data in the game (as it is right now), comment your crazy little idea.