I'm seriously trying to imagine what you would want to transfer between games. What would you customize between games? I hope it's not something as shallow as the sticker system for subspace. Honestly nobody cares about the single player mode, longterm, and creating a custom controller profile between games would take all of 10 seconds per copy. I don't need to transfer that.
Maybe the online win/loss ratio? If the online system is robust, and you gain awards/medals/hats for how long you play, then that might be worth transferring over, but unless it's related to multiplayer, I don't think anyone will care about transferring. It'd be nice if the 3ds one came out first for summer 2014, and then you could transfer your online win/loss records to the wii U one when it comes out holiday 2014.
Anyone else have an idea what you could/would customize and transfer?