I wouldn't say the Junction system is the best system, but I do think it has its good points. First, it is really customizable. You can tailor your characters however you want by using the stronger magic in specific stats. Also, it adds more strategy because you have to look for the better spells in order to actually make your characters stronger instead of just leveling.This game took a pretty different approach from most FF games. Instead of leveling and equipping strong weapons, it's more about the magic and the GFs. Perhaps you find it awkward because it's probably the least traditional.
I think it's best if you have two teams. You should have all your GFs and magic with the main three person team because it is pretty pointless to have it with someone who won't even be in battle. Then when you are forced to change teams, switch everything from someone you were using to someone else in the new group. I believe that's what the switch function is meant for.
Why do you want to change GFs without changing magic? The characters become pretty useless if you don't change the magic to increase their stats.
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