Best GameCube controller for Windows? (late 2016)

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I think it would be best if you bought the original GameCube controller and a Wii U adapter with it. It should work with Dolphin.
You can find the controller and adapter on this page: https://wiki.dolphin-emu.org/index.php?title=Recommended_Accessories
Sure, it's a bit expensive, but the controller is directly from Nintendo.