Im probably speaking for most pokemon fans,we've always wanted to have a Pokemon game..not just another Pokemon game...THE Pokemon game! Anyways here are my suggestions and hope to see's.
Areas ~ The possibility to change regions..from Johnto to Kanto to Hoenn to Sinoh.
~ A battle arena : Battle against other players or NPCs to win gifts or Tms.
~ The Safari zone (Probably in process already)
~ Boss areas : Regi caves,kyogre and groudon areas,Sky pillar. etc...
~ Other dimensions : Space,dream,sky etc.
Leave any other suggestions,thanks for reading!

-Raimu/Vex