The Nuon by default reboots the current game if the stop button is pressed. It should be possible to connect a gpio pin from the microcontroller being installed to the stop button and sink it low when a common button combo is pressed.

Also to expand upon this maybe another gpio pin can be connected to the power button to allow for power off and on through another controller button combo. I found that using 5V+E rather than 5V+VDD will allow the microcontroller to always be powered on. (SD-2300 model)

Using a wireless adapter with a controller would allow for quick remote power on/off.

GPIO pin 2 and 3 are already used by our program so maybe pin 4 for power button and the BOOTSEL pin for Stop button. Using the BOOTSEL so that it being wired to Stop will allow holding the stop button when doing firmware updates.