I'd imagine that the ideal FPS setup for an arcade cabinet would be a Competition style joystick for the WASD movement keys, and a full analog flightstick set up to emulate the mouse, with the trigger handling shooting. The different arcade buttons could be assigned to different functions like cycling through weapons, jumping, activation, turning the flashlight on and off, etc. Although some people don't like to use joysticks for aiming, but there are far worse alternatives. Maybe a lightgun would be good for aiming, as long as you're comfortable holding it with one hand.