Instead of the SD card being the Pokemon storage system, maybe we'll see a new Pokemon Box on the eShop that's compatible with 6th, 5th, and maybe even 4th gens, and there will be the option to transfer through there, with some limitations. This would also enable transferring your Pokemon from cartridge to digital or digital to digital.
A minor issue with transferring is a lack of an input system built into Gen V. This means that an application would need to deal with both builds, such a move limits what you can do with the latter game. --- Thinking is overrated. Like Pants.