Personally, I would add elements to certain characters. Mainly the clones.
For example, rather than all the archers using the same wind attacks, Sakura could have a light-looking attack (like her special), Niles could have dark (because he's from Nohr) and Anna could have fire (also like her specials). I think this would help to make clones feel more unique even if it's purely aesthetic.
I would also want a male Lance user of some sort (I don't mind who). For the missions when only males are allowed, it's much tougher to take down sword users due to there not being any male Lance users.
Also, being able to choose which music track plays on the map would be nice.