There is a problem with this idea : if a player chooses to remove Cloud and Tifa's materias in Shinra's HQ (before the battle against Hundred Gunner & Heli Gunner), you wouldn't be able to reequip them without using Black Choco (the utility) or something. Likewise, I believe that there are scripts that sometimes reequip / unequip materias from time to time (like Yuffie who reequips everyone's materia in a chaotic way, after the Wutai events...).
You'd have to rework a lot of field scripts too, LostWing.
EDIT:
Oops, I see Kuugen already mentioned Wutai. Still, I think there are more.