Thanks for the replies gents- I'm in the UK so it would be to far to post. I will have a think... on which way to go. One thing I didn't check are the new classic nes and mega drive variants the same and on Usb?
@johnodon the extra / is not an issue, issue here is that the core doesn't retrieve the path to your system directory (if it did, it wouldn't try to create this /home/pi/RetroPie/roms/arcade/dc/data directory). My only guess is that there is something wrong with your retroarch configuration/overrides for this core/game (system_directory should be set to ~/RetroPie/BIOS, systemfiles_in_content_dir should be set to false).
If you can't figure out what's wrong in your configuration files, a quick and dirty fix would be to create the /home/pi/RetroPie/roms/arcade/dc/data manually, you'll probably have to put system files in /home/pi/RetroPie/roms/arcade/dc too.
you can't really make these comparisons. atoms and p4s are likely still faster than a single core rpi3 (remember that emulators are almost always single core, and that ARM is way less performant than x86 per MHz, in most scenarios), and ancient versions of emulators were more hacky than 'HLE'. things like ultraHLE (n64) would run on a toaster, but they were barely 'emulators' at that early stage. even today's HLE emulation is vastly more accurate, but needs more juice.
i don't see anyone spending a whole load of time making a hacky model 2 emulator targeted at raspberry pis. by the time they were finished it would be redundant.