Would it be possible to prevent people from using a spell they junction or allowing people to junction multiple spells to a single stat? Think of allowing people to make an Ice mage by junctioning Fire and Lightning to Magic or straight up forgoing elemental magic entirely to focus more on Melee builds by junction them all to Strength. This could be expanded by letting you make real Red Mages and make people more likely to junction lesser junctioned spells to open up more customized spells lists for each character.
That said, I also really like the idea of there only being so many of each spell available among all of the characters, like 9 Fire, 6 Fira, and 3 Firaga, 2 Flare and 1 Ultima with each going up to 100 and tied to your level. This game is a balance nightmare in vanilla, good luck!