Well when you are the first 3D Mario successor to Super Mario 64, you are going to receive excessive scrutiny. Super Mario Sunshine is a good game and I don't think it deserves most of the hate it gets but it has several problems.
It is by far my favorite Mario game to control. You lose some of Mario's combat repertoire from the previous game (punches and kicks), but some of the stuff you can do with FLUDD is just phenomenal. I really love squirting just a tad amount of water in front you, performing a dive, and moving at a fast slide for several second. The way you can combo the new spin jump for either movement purposes (combined with Hover) or combat (combined with spray) is great.
While I don't especially like the art direction in regards to characters and creatures, I love the way the development team brought different parts of a tropical island/resort to life and in a cohesive way. You can even see other levels from different levels in the game, giving each level a sense of place in the grand scheme of the game.
But they really dropped the ball on a lot of other aspects, mostly gameplay related.
Blue Coins in this game are awful. There are way too many of them and no user friendly way of keeping track of what you do and do not have. I also hated that I would get a save prompt every time I picked one up. It kills the pacing, especially when your core movement is so fast and tight.
I don't like the way Yoshi was implemented. I understand they wanted another method to lock content away for you to find and access yourself, but the juice meter was such a weird limitation when Yoshi is already vulnerable to instant death when exposed to water. I also didn't think Yoshi movement was nearly as polished as Mario's. God help you if you have a bad jump when getting to the warp pipe on the island near Isle Delfino.
Some levels, such as Noki Bay, were too large for their own good and made traversal a slog, especially when vertically was in the mix.
There were some questionable gimmicks added to the game that just aren't fun. I really hated the King Boo boss in Sirena Beach. Roulette tied to progression/succession is not fun. Some of the hidden courses/trials didn't feel fully fleshed out either. The one where you are inside the pinball "machine" has some wonky physics. The level that tasks you with riding on a lily pad while atop moving waters and collecting coins while slowly sinking? Terrible. And man, the final gauntlet to Bowser is just a shit show. The way you commandeer the boats isn't as tight as I would like and just led to lots of frustration.
Sunshine is a good game but it has lots of problems holding it back from being anything better.
[EDIT]Added the hidden tirals/courses to gimmicks since I just remembered them after hitting submit.