>>13596886What's most likely is that at some point they'll introduce some sort of eShop transferring app where you upload your Gen 5 pokes, then switch to your Gen 6 cart (if using a cart, since digital is a possibility) and run the app to download the pokes onto your Gen 6 file (after some shitty and completely unnecessary minigame, of course).
If using a digital version you could theoretically have both Gen 5 and 6 in the 3DS at the same time, but since not everyone will go that route, that's why I think the eShop app will be needed.
The only reason I said I'd be disappointed is because if they did have a transfer mechanism in place it would greatly reduce the chances of being able to obtain every Pokemon within Gen 6, but that didn't stop Gen 4 from having all non-starter non-legends available (though I would love for Gen 6 to have ALL Pokemon available outside of transfer or global trade).