When submitting games to Nintendo, developers will be required to tick a box that asks whether they’d like to support cloud saves or not. The options are “Yes, support it” and “No, don’t”. Other than that, no further action is required on the developer’s part.
Now as to why some games will not support cloud saves, a few examples include Minecraft, which has an enormous 1GB worth of save data, and the upcoming Pokemon 2019 games, where the cloud save feature could be abused for cloning Pokemon.
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