I hope it'll be an app where you can put in the pokemon from the currently loaded gen 5 game, then put in the X/Y cart or boot up your X/Y(if downloaded) and access the app ingame. And preferably let us transfer whole boxes at once. That way, only one system would be needed and it'd be nice and quick.
I have to say tough that I found the slingshot minigame to be very fun. Didn't take long either once you got the hang of it.
I don't see why not. B2/W2 were compatible w/ the AR searcher app and they're NDS games.
That's where I got the general idea from. I really hope they take up on that. They made 3DS app and DS game communicate once, it would be strange if they couldn't do it a second time.