The Game Cube controller is great and all for the Nintendo games, like Super Mario Sunshine, Luigi's Mansion and Zelda Wind Waker, but have you tried playing a fighting game other than Melee in it? (If so, it was probably Soul Calibur 2, btw best version because Link)
Everyone and their moms LOVES the Game Cube controller for Melee, I'm not that big into smash to begin with, I was back then, but mostly for the Nintendo Fangasm, which had already died down by the time I got to playing Brawl, I always found the gameplay to be too floaty and much less satisfying than a traditional fighter, now I know there's a lot of depth to Melee with the Wave-dashing and the L cancelling and stuff, but I'm FAR from a competitive fighting gamer, I just prefer traditional fighters because I think they're a LOT more fun than Smash...
Now Capcom vs. SNK 2 and Bloody Roar Primal Fury (which btw is WAY better than the PS1 Bloody Roar games) were probably the GCN games I've spent the most time with, but for these kinds of games the button layout of the cube is just dumb, and the D-pad's position is too awkward to use comfortably, I don't think I've ever had a worse experience playing fighting games, but you know what? I'd say the proper way to enjoy those games is on Nintendont on the Wii, which lets you play Game Cube games with the Wii Classic Controller Pro! Which I still say is the best controller Nintendo made since the SNES (not counting handhelds) because it is the natural evolution of the SNES controller with the D-pad, the sticks, the shoulder buttons and the face buttons are all in the correct place and layout! Granted the sticks aren't quite as good as the GCN analogue stick, but they get the job done perfectly well, and the D-pad is not quite as good as the SNES D-pad, or even on the Wiimote itself, but I've used a lot worse (on the Game Cube) I'd say it's about on-par with the PS1 D-pad, but with a proper cross shape...
Also, Zelda Wind Waker is one of the better 3D Zeldas, it's way WAY WAAAAAAAAAYYYYYYY better than Twilight Princess, that much is for sure, and because of its more cartoony art-style it aged like a fine wine~ (But not as well as 16 bit games)