I think that the criticisms come from very specific levels and a clearly rushed ending. The manta ray boss being one of the worst things ever.
The ending being so bleh makes for that taste being the thing people remember. Not the charm or the tight controls or the cool World building.
I love it, but it makes sense that people would dislike it.
It's not just stuff like Corona Mountain, though it and the final fight are very clear signs of how the game was rushed out the door. There's other signs all other the place that the game was rushed. Like, okay, for Sunshine they decided to have the entire game be themed around a tropical resort. That's not really my thing and I personally feel that the game suffered more for that then it benefited due to the lower variety of levels compared to 64, but there's nothing wrong with the idea in theory. The problem was that not only did they go with a theme for the entire game, but the game had like HALF the number of worlds 64, which reduced the opportunities Sunshine had to show its stuff and combined with the theme made everything feel even more samey and feel like Sunshine had less ideas than it did.
Then, on top of having a lower number of worlds than, they made the decision to not only keep mission types from 64 like the Hundred Coin Star and the Red Coin Star, but had TWO shines dedicated to Red Coin collecting in each world (one in the main world, and one going through the FLUDD-less stage a second time just to collect more red coins). Then on top of that, if you want to go for 100%, you have 24 FURTHER Shines dedicated to collecting Blue Coins, with each one of those requiring you to collect 10 Blue Coins scattered throughout all of Isle Delfino, for a total of 240 Blue Coins scattered through the games world on top of the Red Coin and Hundred Coin stars.
But then, on top of THAT, each world has a new throwaway mission type: the Shadow Mario levels, where you do the same exact thing, just chasing down Shadow Mario and spraying him with FLUDD until he runs away and coughs up a Shine. None of the missions mix it up or do anything interesting at all or have any twists. It's just chase him down, spray him with water, collect Shine. All over super quick.
And the worst part of them is that despite them not being anything great, the entire game revolves around them because they're connected to the game's "story." Like, one of the things I liked most about Super Mario 64 as a kid (and still do) is just how open it is. What's the unlock requirement for the final stage in 64, Bowser in the Sky? Collect 70 Power Stars. Game doesn't really care which ones at all. Got 70 Power Stars? Game lets you in. That simple. Sunshine, on the other hand? Because of the game's story, and it's new revamped mission system, the unlock condition for Corona Mountain is not something like collect 70 Shines ala 64 or a slightly different amount ala Galaxy. Nope, instead, the condition for getting into the (obviously rushed, extremely linear, short, and empty) Corona Mountain is that you have to beat the Shadow Mario mission in each of the games main worlds. And the Shadow Mario mission is always Episode 7 in each world. So, without using any glitches or skips or anything of the world, each time you want to even beat the game, nevermind get 100%, just because of those terrible, throwaway levels that have nothing interesting about them or sets them apart at all, you have to play those same exact seven episodes. at the very least.
Coming from 64, that was a HUGE letdown for me. I loved the choice I had with 64, and that's just gone in Sunshine. Fortunately, it came back in Galaxy, but that just makes Sunshine stand out all the more with just how much it railroads the player among 3D Marios. There's no reason to be that restrictive. Especially since it's not like the Shadow Mario missions (aside from the one at the very beginning of the game I guess and the one in Pinna Park) absolutely contribute to the game's story in NO WAY. Shadow Mario just shows up, you spray him with FLUDD, he moans a bit, runs away, and leaves a Shine behind. That's it. There's no particular reason for story progress to be gated by those piles of nothing and for the mission to be reused each world on top of the existing trope of the (now 2) Red Coin Shines and Hundred Coin Shines aside from Sunshine just clearly being rushed and forced out the door before it was ready due to the Gamecube performing absolutely terribly for Nintendo, and the game really suffered for it (at least it did for me because if I at least had the option of picking which shines I wanted ala 64, that would have added so much more replayability to the game for me due to me being able to mix up which Shines I do and don't collect each time I play through. Instead, each playthrough of Sunshine ends up being pretty "linear" and samey for me just due to that one requirement as there's really no point in even bothering with the other Shines since they literally do not matter in any way unless you're going for 100%).
But yeah, it's so much more than just Corona Mountain and select shines like the Pachinko level or the Yoshi-Isle-Delfino-Boating-Boretacular-Expedition leading up to the stupid leaf-rafting coin collecting mission. There's just so much evidence that the game was rushed through and through and sent out the door before it was ready because of how the Gamecube completely flopped, and the game suffered so much for it, not just in a lower number of worlds, but more reused mission types. That just is what it is, but it being the case, and all of that put together, is definitely why Sunshine is absolutely my least favorite 3D Mario.