Never mind, fixed it :)

I think I'd crossed the streams while flailing at the options. The key is to add -gameio joy to emulators.cfg, so that it reads like this:

lr-mess-apple2 = "/home/pi/RetroPie-Setup/scriptmodules/run_mess.sh /opt/retropie/emulators/retroarch/bin/retroarch /opt/retropie/libretrocores/lr-mess/mess_libretro.so /opt/retropie/configs/apple2/retroarch.cfg apple2e /home/pi/RetroPie/BIOS -gameio joy -flop1 %ROM%"

And then go into the MESS menu and set the analog controls up like this:

ap2.jpg

The key is those "P1 Joystick X Analog" and "P1 Joystick Y Analog" lines - you have to make sure those are set to "None", which isn't the default. Take those two steps and you should be sorted.

@landyvlad yes. There's a menu item at the top of the optional packages to do that.

I wrote a tutorial a while back with some tips to help with the disc swapping and save state mess. https://retropie.org.uk/forum/topic/19269/tutorial-painless-apple-game-emulation?_=1592965674049

One thing I would like to see is write protect in the emulator. Games written in Apple Pascal need the boot disc write protected or the boot hangs. This includes the first 3 Wizardry games. Like I discussed in the tutorial, you currently need to use file permissions as a workaround for this.

@alanhorman pressing f1 would have told you this as well.