I guess it's something like the FF6 (can't remember that well now).
When you had one summon/esper/wtv equiped he had some magic abilities and by using them the players would learn those skills after a while. Then we switched summon/esper to another to learn new magic skills, etc.
This system makes more sense to me, although it changes the concept of the materia as we know.
Now materias work as a recepient where you "deposit" AP to get to XX level. After the materia is in this level anyone can use it in full power. And after getting all materias of this rank maxed, you could get master materia from this grade (green, for example).
Changing to a FF6 system, materias wouldn't have levels, the character would be the one "leveling" his magic abilities. Now instead of being a recepient, materias would be a catalyst to the character so he could learn magic spells. By using a Fire materia for XX time would make the character learn Fire, Fira, Firaga and after that was time to learn from another materia. In the end a character could know all the magic spells (green) without having to use the green materia, however a single/master materia would have to be in weapon/belt to connect to all/elemental/etc.
I kinda used your idea and put it from my point of view sorry
Anyway, i don't know if something like that could be easily done