A few things:

-Get rid of the Magicite system.
Seriously, it sucks. It's might be the hands-down worst character-building system in any of the games. It either makes everyone exactly alike for no cost whatsoever or it turns into a spread-sheet bonanza of who has what and who still needs what (most characters not needing anything, the whole thing is pointless).

-Maybe, maybe get rid of the Fight command for every character.
Yes, gut fight and make their Skills their main offensive use. So, Edgar can only use Tools, Sabin can only Blitz, etc. This way, everyone has their own specific use and the differences feel meaningful. Obviously, the balance and effect of some of these Skills would have to be tweaked in order to fit into the game as is, but as it is there's almost no downside to having Edgar AutoCrossbow everything when you get him. Why even give him a sword?

-Make the game less grindy.
I want to use Strago. Don't make me scour the ends of the earth to get his Blue Magic. It's especially galling since he's a late-game addition rather than someone you've been building since the beginning.

I also want to use Gau. Don't make me spend my whole life on the Veldt battling the RNG to get him the abilities I want. Good lord.