If money is no object You could probably keep it the same size by using an pico itx board and an external power supply. The boards aren't cheap though. Emulating the classics, neo geo, and some fighters would be easy, but the Via Processors won't keep up with anything too advanced.
If you can shoehorn in a micro atx motherboard (or even an itx), you can probably still use an external power supply provided you choose an energy efficient processor (BE-2400, or an EE Core 2 Duo). I can't imagine this would be possible without making it at least an inch thicker, hacking off a parallel port, and/or converting some buttons to the low profile japanese ones.