Don't get me wrong I like the Gamecube controller the best out of the three consoles right now, but it could use some improvements:
bigger d pad
round x and y buttons
a second z button, slightly larger
C stick with a hat like the control stick
It does get some thing right though, it feels great in my hands even after several hours of play, the octagon around the analog sticks is smart, and I like the larger A button.
Making controllers is, I imagine, probably one of the most difficult aspects of console design. You may not notice flaws until hours after play, or only on certain games; durability has to be tested over months and months; and you have to test it over dozens and dozens of sizes and shapes of hands.
Take for example, the X box S-type controller. it seems okay at first but after awhile I notice the feet of the controller are at too wide of an angle and it causes my hand to start cramping. a few millimeters change in the design would have made all the difference.