Satoru Iwata, when speaking at a recent investor meeting has shared that Nintendo is “considering the future possibility of digital distribution of packaged software” for both for the 3DS and the Wii U. This is a fancy way of saying that you may be able to purchase full retail games via the consoles instead of going to retail store.
In regards to the 3DS, they “already have the necessary infrastructure” to do this, and will do the same for the Wii U before it launches, but the decision to launch it:
…must be made by taking into consideration such factors as the relationship with the wholesalers and retailers, and the best way to be embraced by consumers
So, it might not launch with the Wii U unless Nintendo can figure out the details. But it’s still great that this seems like it’ll happening at some point in the next year or so.