I think it is mostly nostalgia. When the GameCube controller was new, most people hated it. The c-stick didn't have as good of a grip as the analog stick. The B button was too small. The front layout was seen as awkward. The Z button felt out of place. Finally, D-Pad was way too small which makes it bad for fighting games.
Still, it was seen as a big improvement over the N64 controller, although the N64 controller was more forgiven because 3D gaming was still a new thing. I would say it was the second best controller of that generation with the Dualshock 2 being the absolute best, the Dreamcast controller being not that good but far from the worst while the original Xbox Duke controller was a monstrosity that was clearly designed by people who had no idea how to design a video game controller. The S-controller was a huge improvement.
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