I never understood this personally.
I think for the most part pretty much every one of Nintendo's Wii successors were better than the GameCube with some exceptions (Wind Waker > Twilight Princess, Melee > Brawl in terms of gameplay depth), and additionally there was MUCH MORE than GameCube too. The GC had a very limited library for the most part compared to the Wii.
Yeah, my thoughts are that the Wii versions of Nintendo's core stable of franchises were mostly inferior. Certainly there are some exceptions.
Melee vs Brawl is up to personal taste, but I think most people agree that Melee is the superior gameplay experience, if you're talking about technical mechanics. Certainly, Brawl had the single-player campaign, but overall the gameplay was slower and just, different. Melee was quick and snappy, hence the longevity of the multiplayer presence and enduring love for that game.
Twilight Princess was on both, but the Wii version launched 3 weeks earlier, because Nintendo wanted to entice hardcore Nintendo fans to buy the new hardware for Zelda, rather than holding off and just buying it on GCN. But, the Wii version has motion waggle, for no other reason than they didn't want to give players the option of playing it on Wii with the GCN controller, even though that functionality was built into the hardware out-of-the-box. As you've mentioned, I think hindsight has also shown that Wind Waker is the superior Zelda from that era.
Mario Galaxy is a classic game, no question, but... that tacked-on waggle. No free camera control. I think with a standard controller, the game could've easily been far better to play, from a technical standpoint. More buttons/ sticks= more ability to control/ manipulate the game. They kind of got there with the Switch port, but they didn't do enough work to rework the controls for a standard controller.
Metroid Prime 3 would have been a GameCube game, but was delayed in order to get moved over to Wii, and again... that tacked-on motion control, at the expense of standard/ dual stick control. And they even added puzzle elements and QTE-type elements that forced specific hand motions, pulling latches, etc. For no other reason than, "Well we have to implement this new controller".
Super Paper Mario was originally one of the last GameCube games, but was pulled from the calendar at the last minute, and moved over to Wii. Again...no more normal controller, now you have to spin the Wii Remote sideways, no more joystick to move the characters, and far fewer buttons. And the game itself, originally meant as a spin-off, rather than the third main entry, sold better owing to the fact that it was an early Wii title with the word Mario in it, and ended up being the downfall of the series, as a result of all of that. But that's a whole other thread discussion. Don't even get me started

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So, yes, the Wii library even just of first-party games ended up being larger, but that's more due to the fact that many of it's early titles were originally planned as GCN games. And add onto that, Nintendo's philosophy during that time changed from making games catering to "core gamers", to prioritizing more casual-friendly games. Which would have been fine, but the change in direction was taken too far, and the casual-first approach of Nintendo from 2004-2012ish spilled over into even their most hardcore, top-tier franchises, including Mario, Zelda and Metroid.
So, whereas for me the GameCube was an absolute pleasure to play, with games specially-made catering to what I wanted. Perfect example: Paper Mario TTYD was the perfect sequel to the N64 original, and clearly designed as a game to please people who mastered the first game and wanted something bigger, better, and more refined and complex. You could make a similar comparison to Mario Sunshine as well, although admittedly that game may have been overly difficult in parts. But overall, it was just a joy to play games on that console. Like the quintessential core Nintendo console, and the peak of what they were doing in their games. Contrast that to the Wii, which for players like me was like, quite the juxtaposition to being more like... "Well, in order to play this game, I guess I have to deal with this Remote tethered to this nunchuck". Thankfully with the Wii U and finally with the Switch, they've realized that many great numbers of players want their latest and greatest games, just not with gimmicky/ tacked-on controls.