What I'd like to see... is something like how Hugh got his starter... was from raising it from it's egg form.
I'd like to see something like that for the player, and just as soon as the player walks to where his Pokémon is, then it shows a silhouette of some shape (where you choose as either Chespin, Fennekin or Froakie) and then taking it with you. And that it would say something that you've raised this Pokémon since it was an egg.
Wouldn't that be interesting? I know it kind of sounds familiar to Pokémon Mystery Dungeon: Gates to Infinity, but I think that would be a great concept.