That is an interesting concept. I have wondered how Final Fantasy games would fare if you could switch the battle system around. For example, a lot of people like the battle system of Final Fantasy X-2. I would love to play a version of Final Fantasy VI with the battle system of Final Fantasy X-2 with party members switching out instead of jobs -- wouldn't that be interesting?
The Final Fantasy VI modding community does a lot of work for this game through emulation and ROM hacking. Major bugs are fixed. There is a difficulty hack that I find myself fond of, not because of the increased difficulty, but because the battle theme does not play when you have a simple enemy encounter consisting only of one or two smaller enemies. This lets you enjoy the music and see it in a whole new light during battles. That's one thing I would change!