TomaTito on 28 January 2016
Nintendo formats every storage device into their WiiU file system, whatever it is. Either way, save data is normally stored together with the game data, for some reason they can't be seperated (only if you delete the game data).
This summer I lost all my Splatoon progress when the external storage got corrupted, somehow my game's content and save file got stored there... Now I store all the save files in the internal memory.
I've discussed this issue with a friend, and we thought that a cloud base system would be great. Then you could load your progress in a friends console; maybe NeXt.
