I know a lot of people like the GameCube controller. I can understand this to a point because the analog stick is excellent and the trigger buttons are fantastic. However, the layout of the A, B, X and Y buttons is so poorly designed that, for this reason alone, I consider the GameCube controller to be one of the worst ever made. I know I'm in the minority there, but that's how I feel. With that said, if you are talking about hypothetical controllers then you could easily switch that layout to something similar to the SNES controller. Make the C stick more like the regular analog stick and add a second z bumper (seriously, why only have one? What were they thinking?)
However, at the end of the day, I don't need a hypothetical controller because the PS3 controller does everything I want in a controller. It has the best button layout; it's lightweight, with a built in rechargeable lithium ion battery, and Bluetooth connectivity. While I'm a Nintendo guy at heart, to me, Sony has always made the best controllers.