I'd be very happy to know if something like this exists as well. Specially for shooters it's a pita to get the controls the right way.

Its definitely possible for homebrew applications to implement a remapper internally, maybe for something launched through it working as a sort of patcher, but it may require some modifications to the wii's system which could prove very very tricky.
Definitely not system wide though. Especially after a reboot.
Your best bet is to use Dolphin with a bluetooth adapter and real wiimote.