I'm thinking Nintendo's plans are to make VC platform independent. Meaning, you buy one on 3DS and you can also play in on Wii U and likewise.
If you notice, Wii U was promised GBA games, yet none exist yet. and the NES games available on both platforms mostly are identical.
Now that NNIDs are on both systems, I'm hoping they begin showing their single account system hands by linking these types of titles across both systems. Makes the most sense and dramatically increases their value.







