It may be just wishful thinking, but they should implement a customization system something like in pokemmo!
Link: pokemmo.eu
With a whole bunch of customization, and some way for premium purchasable items! (Maybe a DLC! That would be awesome! Like new areas on the map, and new stuff to add to your avatar)
They also better have some pretty awesome multiplayer! BW multiplayer was a huge step up from the games before, but something like allowing them to completely come onto your world, plant berries, battle trainers, etc.
Also, 1 really cool mechanic that they should implement, is when you mix records with a person, if they have beaten the champion of the E4 (and you have too), then they will show up as the champion of the E4 (With the team they had at the time of beating the E4, but then once you beat them, the normal champ comes back! Also, if a person wanted, after they beat the game, they could go to a gym with their party containing Pokemon all of that gym leader's type, and they would become a "Fighter" in that gym, and once you beat the game, you could go the downstairs "Fight Club" on each gym, and challenge the trainers who are fighters for that gym That you have mixed records with !