Ipac-2 interface, add wires and DB15 connector.. done. Use the REAL thing, or get a custom joystick.
I've got a raspberry pi2 with retropie - but I'm running an Ipac-4 instead. using a neo-geo controller for my geo games - and nice big captain america 4 player control panel with 6 buttons in the middle two players for geo and other games
lol
make sure you have a keyboard AND also make sure you learn the hot keys or combos to coin-up and start games for neo geo
hold start, left = start
hold start, right = coin-up