I would make each GF multiple classes.

Shiva could be Warrior (strength and Vit), Paladin (STR/Vit + SPR) or white mage (SPR).

A huge factor I would take into account is the special battle command abilities each GF gives. Many of them are near-superfluous, but I would still make them mandatory for each job. That would be a very FFIII-thing to do. I might make Pandemona Dark Knight because I think that's the one with souleater or something like that.

This sounds like a lot of fun. It actually makes me wanna pick up VIII again. I love the junction system.