I don't get when people say that the buttons are confusing. They are still in the diamond shape, but the main button (almost all games use one button WAY more than any of the others) sits right under the first knuckle of your thumb, with the button directly above it under the tip of your thumb. the other two buttons are accessible with a quick trip to the left or right. It is so easy, and you immediately know what button your thumb is on by the shape the instant you touch it.
I really believe that controller preference is largely a matter of opinion, but confusing is about the last criticism I can imagine leveled at Gamecube's controller. I'll give you uncomfortable, since that's purely subjective. I'll give you poor for fighters (though I don't think this is a fair comparison cos you're talking about fighters developed for traditional controllers, but . . . ). But you need help if you find Gamecube controllers confusing compared to others. Can you say R1, R2, L1, L2, X, ---smurfing--- triangle, circle, square?