Yes they will! We've been seeing signs of that already, what with Professor Sycamore ICly offering to send over the Kalos PokeDex and providing an official IC namedrop of the Fairy Type; since the beginning of this overall plot, it's been one of our goals to use it as a way of ushering in the mechanics switch-over to Gen VI proper, so you will absolutely be receiving more information on that very soon! You just have to finish the plot first. o/