According to a Nintendo World Report, in an e-mail from one David Marshall (Nintendo Customer Service Rep) Nintendo is going to attempt to unify the 3DS and upcoming Wii U account systems. No it doesn’t clarify how this will work or if it will include the same content on the respective store fronts, but here is the quote to support the theory.
There is no confirmation from Nintendo proper that this is actually going to happen, but that doesn’t surprise me. We have been in the dark on most of this stuff despite the Wii U’s release ever approaching. If this holds true, maybe that means we will see content that can be shared between the 3DS and Wii U. Virtual Console for both devices sounds like just the ticket for me to pick up both these consoles.