Ok so I've managed to get it to work with wiimednafen, genesis plus gx, Not64 and wiisx, it seems to not work at all with any of the FCE Ultra or Snes9x forks, doesn't work with wiistation even though wiisx works, and I couldn't get retroarch working either, didn't test anything else. The ones that work, work both through the channel forwarder and multi mod manager, the ones that don't, don't work with either.
But with the emulators I managed to get working I can play Genesis, master system(genplusgx and mednafen), NES, GB/GBA, PC Engine(mednafen), playstation(wiisx), n64(not64).
The issue is, I can't play snes games since snes9x doesn't work, anyone got any ideas on what to do about these? I couldn't get retroarch working, and there seems to be no other option besides snes9x and retroarch.
EDIT: Ok managed to get retroarch working, at least on the menu, I remade the channel forwarder and it's working this time though I'm not sure what I did differently, but now I'm getting a "Exception DSI ocurred", but that doesn't have anything to do with fakemote.
EDIT2: Wel I finally got everything working! Turns out the issue was with retroarch itself, the latest version v1.20.0 crashes when trying to access the sd card or usb drive to load content, I downgraded to v1.19.1 and now everything works! Finally I can play every system I want with the dualshock4!