I would feel much safer if I was able to redownload my eshop titles to a new system if it gets stolen or the SD card gets lost. If I were to lose it with a physical cartridge, I would only lose one game. This could make a lot more people confident about digital purchases as well. Right now, buying digitally is not financially smart (same price as retail, no resale value, no game case, no sale chance, no security, etc). Also it would be nice to have cloud storage of save files as well. That or be able to create backups.
Every other company uses an account system or gives incentives for downloading digitally. Nintendo, please use modern policies! It would cost very little to implement these changes, and profits for downloaded titles would undoubtedly increase.