With every Nintendo-published title being released on the eShop the same day as retail, I think it's safe to say these will be too.
I'll probably get Y digitally and X in-store. Pokémon is pretty much the reason why I play Nintendo handhelds, I'd probably want access to it whenever I have my 3DS. In addition, I'll probably be able to play it 12 hours earlier than retail (my EB Games never does midnight releases for Nintendo titles).
I would, since I'd be certain to keep the retail copy for seven or eight years before selling it, but I don't like the idea of something as important as a Pokémon save file being tied to my hardware, what with the limited number of system transfers that can be done.
"Cats...are kind of like girls. If they come and talk to you it's great. But if you try to talk to them it doesn't always go so well." --S. Miyamoto