you have to design your game for the GameCube controller or else its not going to work out well

This is true for basically every console since the N64

While not that much of a problem during the 5th generation of consoles since each side had their own unique controlling method and there weren't that many multiplatforms, it definitely started to hurt once the Dreamcast, PS2 and Xbox started to have similar layouts

It seems that Nintendo never realized that by going unconventional for one or 2 games they were damaging their entire console by making multiplatform developers alienated with their consoles, since they could only choose one of 2: either change the controls specifically for the Gamecube or just leave it like that, and since developers hate giving each individual console special treatment, most left the controls just like they were in the PS2 and Xbox version

From the top of my head:

The N64 controller was made for Mario 64 and probably Ocarina of Time, though Ocarina was definitely fighting the controller and trying to get the most use out of it

The Gamecube controller was made for Wind Waker and Super Mario Sunshine, Melee is definitely fighting the controller but people adapted to it

The Wii controller was made for Metroid Primer 3 and Skyward Sword (with Twilight Princess quickly adapted for the Wii)

The Wii U controller was made for... I dunno, Splatoon seems like a stretch since its main gimmick could have been implemented on a regular controller that has a gyroscope or a motion sensor (Steam Controller for example)... Heck, out of all the consoles since the N64, it seems Nintendo though the less about the Wii U than any other previous console and they cared more about being unique than actually thinking if it was a good idea