Well, you can use a smaller trackball made for a cocktail table to save space there.
If you really want to have a lot of different controls then just make one continous control panel that goes all the way around the machine.
Or duplicate the Cinematronics cocktail design, as the control panels are full size, so each end should have room for several different controls.
The Cinematronics cocktail design should have enough room for a 4-way, an 8-way, a trackball, and a spinner. And it fits a 19" monitor easily.
I would use this layout method myself.
Side one (read left to right).
4-way,8-way,6 buttons, trackball
Side two
4-way,8-way,6-buttons, spinner.
Putting a 4-way and an 8-way on each side will allow you to play all the cocktail mode games correctly. Obviously 2-player simulatenous games are mostly out of the picture.