It would use a personal cloud service account you define. For starters, Google Drive. I would add others like Amazon Cloud Drive, BOX, OneDrive. Google Drive is the "big one" as anyone can register for a free account, and 15GB is more then enough space.
What I had in mind is having it compare your saves on your system with that saved in your cloud account, and then it would push any saves not already on your cloud service account and then pull any saves.
The idea would be I could play a game on one 3DS, sync my saves and then if I were to start playing on another 3DS linked to the same account, it would pull the save file.
It would handle conflicts and let you decide which save to use.
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BTW, I'm a KODI cloud service developer. So I'm very familiar with how to get this done on the cloud-end. I started messing around with compiling on the 3DS and think I can learn enough to get the device-end part done.