Honestly what I think they should do is give relics and equivalent tier weapons a unique materia slot for a special new skill materia. Every job has a selection of such materia that directly modifies their skills in some way. Since there's only one slot on the weapon there shouldn't be any balancing issues as there are no combinations to account for.

Beyond that it would be nice to start seeing 'sets' of materia for armour with stacking bonuses for every X number of them you have melded to your equipment. Again very simple to balance given that it's standard for the genre (seriously almost every MMO out there has set bonuses in some form).

I'm with you that materia is the way to solve the itemisation problems the game has. 3.2 is adding materia to tomestone gear as well so it seems SE is experimenting with the idea in some form. We just need some new, unique materia types.