I'm also having the same issues.

Wii Remote + Classic Controller pairs correctly, is configured and works in EmulationStation. However, it fails to work with games. This is on the latest 4.1.

I also had an older image of some 4.0 beta where the Wii Remote + Classic Controller combo worked with a bluetooth dongle. After updating that image to the latest 4.1 (to use internal bluetooth), the controller was only partially working. In particular, I had the following issues: 1) games recognized the controller as Player 2 (might explain why it doesn't work with some games), 2) Hotkey button was not working although configured properly.

Since the controller appears to pair correctly, maybe this is just a configuration issue. Unfortunately, if the controller is not recognized in game (or the Hotkey button doesn't work), I can't even use the retroarch menu to reconfigure.

The Wii Remote + Classic Controller is such a great combination for retrogaming. It would be really great if someone from the Recalbox team or someone with more expertise could chime in on these issues. Thanks.

Hi!   I encountered the problem playing Snes and Mame games.

Hello! I've been using recalbox for about a month and I love it!   I've no issue with an iBuffalo Snes controller. Recently I decided to pair my Wiimote in order to use my Wii Classic Controller Pro (like this one). The first time the system recognized three controllers: Wiimote, Wii Classic Controller Pro, and Playstation 3 controller. After a reboot the PS3 controller went away, so that's okay now. I configured the Wii Classic Controller Pro in EmulationStation and assigned it to player 1. Everything works fine in EmulationStation and games work fine with the D-pad. However, when I try using the left analog joystick the up and down directions are reversed. I tried configuring it again pressing down on the joystick when asked for the up direction but that didn't change anything. I also tried following the suggestion given at this topic which seems to have a similar issue with a different controller, but that didn't work either.   The issue is present in v4.0.0-beta3 and v4.0.0-beta4.   Thank you!