So, I just managed to get my hands on an XE-1 HE PRO joystick. I rather like it. It's for the PC-Engine, but I am curious if it can be modded to USB, or if there is an adapter out there. I've looked around and haven't seen much, but will keep searching. I'm pretty sure the PC-E uses the same socket as the pre-USB Apple Macs, if that helps.
Like any other joystick you can replace the PCB with another one, to get it to USB. As long as there's enough space inside (depends on your other PCB and how much work you're willing to do) it doesn't have to be much space.
Data on the actual protocol is here and info on how to convert it to parallel port is here.
Goto the RetoZone and buy a TurboGrafx retrokit. I'll work for any pc-engine joystick but you need to match the PCE pinout with the TG16 since they're in different order.