More cross-customization between job classes
I liked the FFT aproach where not only can you pick an ability set, you can pick a support ability, counter ability and move ability. While this exact set of 4 probably doesn't fit into the game mechanics of FF5 as well there are many variations on the theme you could chose. (Maybe secondary ability, support ability, equipment, special ability (could be things like dash, see hidden walkways, show enemy HP, etc))

Graphics ala FF3 & FF4 DS.
Controversial to some, but I liked them.