Not sure if it's been mentioned again, but having only a VGA output is seriously limiting options for some setups, especially mini desktop cabinets which usually use composite or S-Video only LCD panels. Having DVI-D would also be great because VGA sucks. And yes I realize the irony of that statement after asking for composite and S-Video outputs.
And about the whole "automated" cabinets with rotating screens, dynamic marquees, auto 4/8-way joysticks, lighted buttons, etc... keep it simple.
For example, dynamic marquees can vary in aspect ratio, in resolution, in color depth, etc. Dynamic joysticks may not be limited to 4/8-way, etc.
So as I said above, just send the ROM filename on a serial port or SPI pins or something, the external peripherals controllers will take care of their own stuff with their own internal settings for each ROM filename. It's future-proof, upgrade-proof and allows all kinds of customizations.