I want them to do something similar to a Save transfer for Pokemon X&Y.
Since they'll probably bring back costume changes and some of the other X/Y features, pull an animal crossing and allow your XY trainer to go to Hoenn and gather badges/pokemon, and do quests/buy clothes/etc. And be able to transfer that [parasitic bomb] back into XY, which they could totally do because all the Pokemon are already in there and they could easily patch some extra stuff in.
But of course only have it as either a New Game + or as something in addition to the main game.
And of course, who's to say they couldn't do that vice versa, after clearing Hoenn have that trainer go to Kalos or something.