Nintendo has said that they really like the GC controller's layout and would like to stick with it in some form or another, and it really is basically the same type of design that's out there with the other consoles. 2 analog sticks, some buttons, some shoulder buttons. They may add more buttons, but, err, that makes it easier to play older games, not harder. Think about it -- they have a Z button, so they also have a, I don't know, Q button, over the left shoulder button, so you have Z and Q. That doesn't affect older games. Say they include some buttons on the inside "wings" where you grab the controller -- older games, and arguably some newer games, won't use them, so no problem there either. I mean, look at the games out now that don't even use X, Y, or Z. and hey, the next controller may even have a larger D-pad.
They'd only have a problem with backwards compatibility, it'd only be if they got rid of one of the analog sticks, or dropped half the buttons. I don't see that happening.