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Though the Wii U's Virtual Console is far from perfect, the implementation of the actual games is nicely dense with features. I just downloaded Balloon Fight, and found a surprising amount of control customization available to me.
By tapping the touch screen (ZL+ZR also worked), you can access the Virtual Console menu, which allows you to create a restore point, reset the game, or change controls. From there, you can alter the individual button mapping for any controller you have plugged in: I tried a GamePad, Wiimote, Wii U Pro Controller, and Wii Classic Controller, and each let me set the function of every button on the device. The GamePad, Wiimote, and Classic Controller all served as the player 1 controls, and the Pro Controller defaulted to player 2.
