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Super Mario Sunshine in Super Mario 3D All-Stars doesn't support the GameCube controller
A sad note for purists
You can plug a GameCube controller into the Switch if you have the GameCube Controller Adapter, and numerous games can be played using it, albeit with limited functionality. Unfortunately for the Super Mario 3D All-Stars version of Super Mario Sunshine, that's not going to be the case.
The official Japanese website for Super Mario 3D All-Stars clearly states that the GameCube controller is not supported in Super Mario Sunshine. While we're not 100% clear on whether that means zero support or very limited functionality, it seems you won't be able to play as you could on the GameCube with all the GameCube controller features.
[Link]