I've got a few suggestions. :3
menu hotkeys - eg. "P" for pokedex; "O" for social; "B" or "I" for bag; etc.
use of healing moves outside of battle
pokemon nicknames
ability to re-order pokemon moves via drag 'n drop
if possible, double head slots for clothing items
TRADING house
equipable expressions
option to hide player names
make dig, surf, and any other out of battle moves that require dialogue like the moves cut and rock smash (eg. no dialogue)
make TMs infinite use like HMs
drag 'n drop vendor system
ability to change user name
ability to release pokemon in the field
passive health and pp regeneration
reduced cooldown on rebattles for members
item sorting
better scrolling in the pokedex
barbershop\change hairstyle in coin shop
game specific mouse pointer
everstone
bike/mount in caves
secret bases