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

I agree with all of these except for the infinite use TMs. They are too much of a needed gold sink. But I do believe all TMs should not be a 1 time aquireable item. You should be able to farm or buy all the TMs that exist, although some should of course be tougher to obtain.