In a short video update only released on the 3DS eShop in Japan, Satoru Iwata has confirmed that a 3DS Data Transfer Tool will be available in the region from March, which will allow for save data from retail cartridges to be transferred to retail download software.
In practice, this may not be a tool used a great deal, though it'll undoubtedly prove useful to some. If you have a save profile on a shared physical copy of a game such as New Super Mario Bros. 2 but pick up the download version, this should allow you to easily transfer that data. Details were slim, however, though it doesn't seem to have been suggested that the tool will do anything silly like delete the save data from the retail cartridge after the transfer.
As this was a video only released on the Japanese 3DS store, we'll need to wait for details on a Western release. We anticipate it will arrive in due course, but due to the comparatively rare occasions where the tool will actually be put to use, we doubt it'll be a major priority for the big N's regional teams.
If you want to see the video — even better if you speak Japanese — you can check it out below. In the meantime, let us know whether this is a feature you can envisage using in the future.