Okay, I just finished experimenting on my own control panel. I played Gauntlet and Simpsons. Here are my impressions:
It's a tough call. On my control panel, the red joystick (in the picture in my previous post) feels very natural being angled at 45 degrees, while the green joystick feels a little strange at that angle. I think the reason is that the red joystick is further toward the back of the control panel, so the joystick itself is at more of an angle to the monitor. The green joystick is at less of an angle, so the 45 degrees isn't as intuitive.
When I first built the cabinet, I had the joysticks in the same positions, but they all faced forward, and the red joystick felt really wrong. I probably didn't pay much attention to the green joystick, I probably just thought it would be the same way, so I changed both of them.
No conclusions from all of that, it is just my observation, having just tried it with an eye for the problem. I am currently designing a new control panel, and this is definitely something I will think about in the design. One more problem to struggle with.
I would be interested in finding an old Gauntlet machine and trying one of the side positions to see how it feels. I'll have to keep my eye out for one.
-Jeff "etumor" Allen