Okay, took a look at the Joystick ports on a Linux system today. It seems to me the Retrode2 is not reporting the joystick devices properly.
Here's what happens (with current 0.18 firmware):
HID Mode 1:
"4 USB game controllers plus mouse"
The devices are NOT reporting themselves as joysticks / joypads.
Therefore, only the mouse is found - and the rest appears
as /dev/input/eventx in Linux. They should appear as /dev/input/jsx,
but apparently Linux does not recognize them as joystick.
HID Mode 2:
"2 USB game controllers. The left Sega and SNES ports are both mapped to
controller 1, the right ones to controller 2. Up to 2 players."
In that mode, the Retrode2 appears as ONE joystick (/dev/input/jsx)
with lots of buttons on a Linux system.
Both the DPad for the left and right controller ports appear as the
same axis, the left controller uses Buttons 1 - 8, the right one higher
numbers.
So the joystick setup is something that could need a fix in the
firmware to properly work with Linux.
Ideally in HID Mode 1, it should appear as 4 joysticks and a mouse. And
in HID Mode 2 as 2 joysticks.
I haven't tried the N64 sticks yet, but the analog stick should also
appear as analog stick I guess

Hopefully, it's just a small fix that's needed in the firmware - maybe
just some USB description is wrongly setup.