That's a good point and something I've considered. Perhaps a version 2 candidate which I'll elaborate on further down. For now things are laid out according to PCB design considerations. Power is situated close to the source, video and audio lines are well separated and insulted via a large ground plane and so on. Also size of the PCB has been kept minimal to keep costs down. Sometimes there's a trade off between what's best physically and what's best electronically, if that makes sense.
I'm actually toying around with another design concept in the background. I'm developing it so that everything barring controller inputs is on the main PCB. By everything, I mean all power, audio and video outputs (including RGB, s-video and composite). The controller inputs will be a completely separate PCB that docks on top. This will allow for let's say Neo-Geo and Mega Drive controller inputs on the one board. I can add rapid-fire and kick harness support. I can develop different controller boards for say Snes or Saturn or perhaps 4 player output and the end user can simply swap boards out pending on which controller scheme they would like to utilise.