I'm in the middle of the same type of project and I was stuck on the controller board as well.
First I've tried with a Teensy LC and a Arduino Pro micro but I'm having issues with the joysticks after using both regular analog joysticks and PSP1000 joysticks.
Finally to get some evolution on the project I've went with the classic SNES controller USB version and I've cut, split and rewired it and it works like a charm
Steps taken:
- most boards are single layer and top surface leads so I scratched of the paint where I though I would be rewiring (before cutting the board)
- test the leads are correct with the multimeter / continuity test
- cut the board in pieces
- Rewire the leads you've tested and voila
You will need to rewire the usb leads straight to the Pi but I don't see any issues there
here's a quick picture of what it looks like in the end
1 part for the arrows
1 part with the microcontroller in the middle
1 part on the right for the action buttons