I think the hid_nintendo driver works for USB connected gamepads, but it seems your controller is not 100% compatible with the Switch Pro Controller and the driver doesn't add the device.
You can check if the controller is properly initialized by running via SSH:

dmesg -w

and then re-plugging the controller. There will be some messages from the driver - if there are errors, then it means it's not working properly and the input device doesn't get added. If that's so, then I'd get a different controller, one that's advertised of working with a PC also - not just the Switch.

Hey, thanks all. I changed this around as suggested and it worked.

Button 5 is real block and 6 is "quick block".

The installer looks pretty simple - did it create the retrogame.cfg file in /boot ? Are you running the installer as root (via sudo), as indicated in the instructions ?

More info-

I've confirmed holding the buttons down works in general. I played GIJoe and got the auto-fire and just held the button to get it to continually fire. So it works in theory and works on my cabinet.

Could it be specific in some way to MK2 - nvram, cfg or DIP switch settings?

I'm also not insane, right? Holding block in MK2 should keep the character's block held?

@Merktheluddite

please fill out https://retropie.org.uk/forum/topic/3/read-this-first

i notice sometimes afrer going into the menu to do some maintenance or playing a certain game, the buttons will TOTALLY reasign themselve

we're going to need an example

As @mitu said. The reason behind it is that the mappings are stored under the name of the controller in the directory /opt/retropie/configs/all/retroarch/autoconfig/. Thus, if you have identical controllers, only one mapping will be stored for both of them, and if their wiring is different, their common mapping won't fit one of them.

edit: "will be" -> "are" + "doesn't" -> "won't" 😉

I think I've found the issue. There are two connections on the button as well as ground. I've switched few of the buttons over to the second connection and they all now function as expected. The ones I haven't changed still result in continuous firing.

I'll continue to rewire and report back if the results are good.

We all miss things. That’s why being on this forum is great. If one of us misses something, someone else will pick it up

@clyde I try to create such a config file there with the output from jstest. All buttons are recognized, even the coin input gives feedback. It already helped to try on. Thanks very much, I get back later...

Edit: unfortunately no. My resources are very limited, I'm actually in the Philippines for holidays, building this machine for my friends bar. Brought all electronics from CH but no controller. But now time starts running out :-( glad that at least there's no power outage for days and internet is working...

Edit2: I copied the cfg of the Logitech gamepad to something like joypad.cfg, commented out most of the lines and ES doesn't ask anymore. Joystick works, most of the buttons too. Not sure if retroarch takes this config for the games now, but that will be sorted out tomorrow. Was a great help to get here, thanks again.

@mhutter please, paste the content of these files in ghostbin.com (or something similar):

/opt/retropie/configs/all/retroarch-joypads/NAME_OF_YOUR_JOYSTICK.cfg (more than one file). /opt/retropie/configs/all/retroarch.cfg /opt/retropie/configs/nes/retroarch.cfg

My problem is fixed, just had to connect to wifi, get things fixed and i'm done! Thanks for da help!