I'm not a Wii programmer but I am a grad student focusing on operating systems. I can tell you that the difficulty of what you are asking could be very high depending on how the Wii currently handles input. Back on the game consoles old enough for me to understand how they work (about as far back as the first Playstation), events like controller input are routed directly to the game software without an intervening OS touching it at all sort of like how DOS used to handle things. If that hasn't changed, then there's just no good way for Nintendo to insert software code between the hardware event/interrupt and the game software that's in charge of handling it.Originally Posted by the$#!Za.
If the Wii acts like more of an OS in the desktop PC sense, then the Wii OS handles input and passes it on to the game program. The biggest advantage of doing things this way is that it works better in a multi-process environment. Given how the Wii doesn't spend much to any time running multiple programs at one time, I doubt they've invested in the overhead to implement such a system. Even if they did, it would roughly double the response time to add a translation layer that's transparent to the game program layer.
Either way, it's a LOT better idea for the game developers to handle the input mapping then it is getting Nintendo to handle it.