I like using the Classic Controller Pro, too. To be honest, the GameCube controller is one of my least favorite controllers of all time. The GameCube controller feels clunky and awkward, and the button layouts are really unbalanced. The only thing I like about the GameCube controllers is the smooth L and R buttons, but the controller gives me hand cramps and feels considerably worse than many other controllers that I've used.
I love the Classic Controller Pro because it feels like I'm actually using a traditional controller. Like you said, the layout uses the SNES controller as it's basis, which is always a plus because the SNES controller is one of my favorites. The control sticks have a more smooth grip, the d-pad (while not used for Super Smash Bros. much) is much bigger and better than the GameCube's d-pad, the button layout feels much more accessible than the GameCube's layout, and I like how it's easier to reach between ZL/ZR to L/R (which makes it easier to grab or shield). I even use the Goldeneye 007 Classic Controller Pro, so I get a lot of comments on it and it's a great topic starter. If the Classic Controller Pro was wired, then I would definitely use it in tournaments, but unfortunately I have to use the horrendous GameCube controller instead.