Affeinvasion
Member
I doubt there will be transferring from app -> G4/5, only G4/5 -> app.
Probably the app will be able to poke at the game data directly, just like Dream Radar was able to insert Pokémon into your B2W2 games. I think that should be a significantly different process, technically, from connecting a DS game to a 3DS game wirelessly.
There's no reason that they can't make a pokemon box type app that dumps your pokemon data from a DS cart into the app which can then be transfered to X/Y.