http://www.change.org/en-GB/petitions/nintendo-stop-region-blocking-make-the-3ds-and-wii-u-region-free If you want to play all your favourite Japanese games on your PAL console, then sign the petition
I'm not a programmer but I think this issue is due to different BIOS' released to different countries. If it is then, they can just provide upgrades to the BIOS but that would provide opportunities to acquire their BIOS much easier.
and who makes the bios? the console manufacturer. Region locks are entirely artificial and unnecessary these days