Save files will most likely be transferred via an SD card, and the games will be downloadable. Seems like the most logical option to me. Otherwise, the save files would need to be uploaded and downloaded again, which would be quite ridiculous. Then again, it's Nintendo and their - at times - extraordinary strategies. Hmm.
Not only that - giving the user the possibility to transfer the game from one DS to the other (3)DS will give hackers the perfect opportunity to dump DSiWare, which is not in Nintendo's best interest.