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Has Nintendo shut down a game because it cloned the gameplay of one of their games?
(programming.dev)
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Almost everything they've taken down has been for name/character/assets reasons: Pokémon Uranium, AM2R, etc. Something like Ship of Harkinian, a source port of Ocarina of Time, doesn't provide any Nintendo assets and hasn't been taken down yet. To my extremely limited knowledge, gameplay generally isn't copyrightable unless it's specifically been patented for some reason, so I think you're in the clear.