For Wii:
You can remove mload and just use ios58 for USB support. In Makefile, remove ehcmodule.elf. You also have to remove all references to mload in neocdgc.c.
It seems you still have an error with dirnext etc. You can copy some parts from this code:
https://github.com/emukidid/neogeo-cd-redux/blob/master/src/fileio/sdfileio.c
Fo GC:
I have to admit that it was never intended to be GC compatible. As the name suggests, wpad_keymap is related to wiimote only.
I started to update the code some time ago, and wanted to look at this bloody video bug again. With recent libs this is worse because it's stuck at banner loading!
To be honest, instead of the buggy neocd-wii(and the poor code I added) I think it'd be better trying to test this:
https://github.com/libretro/fbalpha
NeoGeo CD is available in this core and they added music support recently. That's the good news!
I've tried to compile it by hardcoding the subsystem value. With the latest Retroarch, the games start but no music or crashes when loading .cue file. With an older Retroarch version, it starts with .cue + wav but it crashes when another track is loading... Well, it seems there's a curse around Neo CD and Wii!