Yeah, I proposed the ability to use either the Wiimote/nunchuk or the Gamecube controller in another thread, but people there brought up some good points.
It would make developing a game take a LOT longer because they would have to program for two completly different controllers. This would mean twice as much testing, bug fixing, etc.
This would also mean the cost of making a Wii game would increase and that's not good because Wii is has a lot of publishers intrested thanks to Wii not needing features like 5.1 Surround Sound and HD content.
Thus, developers could also justify charging maybe $60 per game like Xbox 360 and (presumably) PS3 will.
Personally, I would like the option in cases where a game developer doesn't do a very good job utilizing the wiimote/nunchuk controller (which will inevitibly happen).
Who knows, I might be wrong about the problems it would cause and in that case, I would be even happier with Wii.