We don't know if it's possible and probably won't know until August/September, so we have a lot of time to discuss this.
Dream Radar proved that 3DS games can access DS saves, so it isn't too much of a stretch to say that X/Y transferral could rely on a Gen V game being in the cartridge slot. The obvious side effect of this method would be the lack of this feature on physical copies, but it's the easiest way to do it.
Alternatively, since most 3DS owners also own a DS or second 3DS, a method similar to the Gen IV to V method could be used.
It'll most likely be the same method as Gen 4 to Gen 5. 3DS doesn't have the ability to save files and the games turn off if you remove them. So the only thing I see happening is the same link up as Gen 4 to 5. Two DS or 3DS' one sends out a signal and links up with an older game, then you select and send them over.