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If Game Freak really wanted to prevent that, they would have the save file be stored in the system itself as opposed to the SD card, which would be rather forced.
That's different since the game wasn't downloadable and, generally speaking, Wii save data couldn't be stored on the game disc and so the system was used. SD cards were optional, whereas now they're required for eShop downloads.Nintendo did it with Smash Bros Brawl, so there is precedent.
Game Freak said:Just one save file. With Pokemon games, we always just want to make it one.