It would be nice if character customization were expanded to allow players to further customize their character's physical appearance—e.g., change the character's body and facial structure (to a degree), eye shape, mouth shape, etc. I would also like a greater range of hair colors and hair styles from which to choose, especially for the male player character.
I agree that version exclusive clothing needs to go. I remember looking at Serebii's list of available clothes when I first got Sun and wanting certain clothes, only to discover they were only available in Moon. I would also like more clothing options, at lower prices.
I think costumes based off past generations' main characters would be cool, but it's not really necessary.