The gamecube controller sucks when playing some games, as mentioned in this thread. I think Nintendo should add a controller configuration option, that would solve some problems.
i liked all the newer gen controllers... GC/XBOX/PS2, all had way cool controllers... they all have pretty much the same button layout, its just a matter of personal comfort...
a smart 3rd party company would make a controller of each style thats universal, so you could take your favorite style and use it on each system... granted there probably isnt a ton of people with more then 1 system but the ones that do are willing to drop the cash to make it worth it.