Something they did again with Twilight Princess, which is still a Gamecube game through and through.

In retrospect, Gamecube-era Nintendo looks to me like the time when Nintendo was experimenting with the stuff others were making standard in their games (the blue coins nonsense collectathon, for one) and apparently getting it wrong and/or making it intentionally more janky and pointless than it should be. Noki Bay could have been as good, but it's so full of nothing. Fantastic architectures like Bianco Hills and Ricco Harbor could have been exploited to further greatness, and they're already pretty much the best levels in the game, the most 3D Mario-like.

Gelato Beach is pretty much wasted space, as most missions takes place in a very limited part of it (the red coins come to mind) and the level is pretty small anyway, so missions that have you traversing it are full of jank and very frustrating stuff (the melon 'escort mission' with those cataquacks, urgh). Worst thing about Sunshine is that there isn't a single level that doesn't have at least a disappointing mission that makes the otherwise overall good level design completely redundant.

Super mario sunshine flash game