Because of how exaggerated the Kangaroo Court is at the beginning of the game, some believe the Piantas just saw Mario as the solution to their problems and slapped him with the court sentence to make sure he'd stay to fix them. There's also a group of Piantas in Paper Mario: The Thousand-Year Door that are clearly running a crime syndicate, which does little to dissuade such interpretation.
The Piantas and Nokis are not hoarding Shine Sprites; rather, the Shine Sprites are simply hiding nearby and are only willing to reveal themselves to Mario when he performs a good deed for them or satisfies their challenges because the Shine Sprites need to determine that Mario is trustworthy.
Badass Decay: Bowser had gone from an imposing antagonist in 64 to a goofy dad with an easy final boss fight. Thankfully, Super Mario Galaxy rectified this and made Bowser and son more foreboding.
Captain Obvious Aesop: There's two "no der" moments that occurs in the game by FLUDD. In one level, after you clean an eel of its bacteria-ridden teeth, FLUDD tells the player to always take care of their teeth. In another level, after you get the baby Chain Chomps into a pool of water so they can cool off, FLUDD informs you to always be kind to your pets.
Is the shift in direction from the openness of 64 to the more linear Sunshine a good thing?
Critical Dissonance: Sunshine got excellent reviews, though not quite as good as the other 3D Mario platformers. To this day, reception among fans remains far more mixed due to the corny cutscenes, Bowser's Villain Decay, and the removal/replacement of many of Mario's moves from Super Mario 64.
Demonic Spiders: Red Cataquacks. They'll toss you into the air just like the blue ones, but will also take away 1 health every time they do. They also tend to come in flocks, and you won't land far from where they tossed you. Getting stunlocked is all too easy. And good luck trying to complete the last mission of Gelato Beach, as there's a dozen of them waiting to ruin your day.
Disappointing Last Level: Corona Mountain is rather short and empty, and the unorthodox controls of the wooden boat that has to be used at one point makes it harder than necessary.
What kind of goop tastes like an ice cream flavor? Are we sure we're cleaning off pollution or a little kid's favorite 31 flavors? For reference, when the Pianta statue is submerged, a Toad can be found stuck in the goop; clean him off, and he talks about what the goop tastes like.
Because the precise details of the transaction are only cryptically alluded to, the revelation that the Paintbrush was an invention of Professor E. Gadd's has led fans to come up with many an Alternate Character Interpretation for him.
That Peach had to think about it for a second when Bowser Jr. said she was his mother got a lot of people wondering why she had to think about it.
Fanfic Fuel: Il Piantissimo finding Bowser Jr.'s paintbrush at the very end of the game could lead to some very interesting ideas for a sequel...
Fanon Discontinuity: Despite Bowser admitting that Peach wasn't Jr.'s mother, and Jr. admitting he knew this all along at the end of the game, many fans don't believe this or try to find ways around this. Others simply find it highly suspicious that Peach didn't reject this outright or react like a normal person would when told such a ludicrous claim, which has several fascinating and disturbing implications that she may have done something similar even if the specific claim turned out to be false.
Franchise Original Sin: This was the first 3D Mario Platformer to have Mario die if you fail a minigame. This would be carried over into latergames, except this time he can be in the air and fail a game. This was reversed in Super Mario 3D World, as running out of time in a Mystery House challenge simply resets the event chain.
Fridge Brilliance: If you remember the true ending of Luigi's Mansion, which came before Sunshine, Luigi managed to make his haunted mansion not haunted. He apparently remains there for the events of this game, which may explain why he was nowhere to be seen in Sunshine.
"Funny Aneurysm" Moment: Many fans thought the flooding after you complete all the Shadow Mario missions was funny. Then Hurricane Katrina happened.
Goobles, the pudding-shaped creatures that spontaneously arise out of any goop that's lying around.
The bees, usually because they're always hanging out around narrow paths and tend to knock Mario off of them. In one instance, they're guarding a red coin on the edge of a cliff. Made even worse by the fact that they're tiny and incredibly difficult to see when there's only a few of them left in a hive. And your only defense against them is Yoshi juice.
Cataquacks, because their sole purpose seems to be to annoy you. If you get one's attention, it'll chase you around, trying to toss you up in the air. If you're really unlucky, you'll land close enough to it that it can do it again. They're everywhere on Gelato Beach, and the only way to kill them permanently is to knock them into the sky with Dune Buds or by eating them with Yoshi. They get upgraded to Demonic Spiders in the Watermelon Festival, as they'll do the same to your watermelon, destroying it and making you start over. Also, the red-colored ones can deplete your life energy.
Idiot Plot: Bowser and son's plot to frame Mario would work only if the Piantas were stupid enough to confuse an obviously blue Shadow Mario with the real deal and ignore that Mario has an air tight alibi of being in an airplane with multiple witnesses, one being royalty. Unfortunately for Mario, they are. Even when they can see the real Mario chasing a Shadow Mario actively spreading graffiti right past them.
Bowser's voice acting and dialogue make him seem less like a giant scary Koopa and more like a goofy sitcom dad. In fact, most of the voice acting is really lousy. And Bowser would remain that way until Galaxy.
FLUDD's Disney Death at the end is just goofy and pointless.
The commercial for the game featured an incredibly cheesy, environmental song.
Narm Charm: Bowser's voice sounds draconic enough to work, and some people consider it to be just plain awesome.
Never Live It Down: Peach hesitating to answer Jr's assertion that she's his mother caused most gamers to believe that this is proof that the Princess is a Dumb Blondenote The complaint is along the lines of the idea that since she knows she's not his mother, there was really "no reason" for her to ponder this fact for any amount of time, and that she should've immediately tried to correct Jr, or at least shouldn't have said "I'm your mama?" as if it were remotely plausible that's no good for anything other than being kidnapped. This is despite Bowser telling him she isn't his mother and Jr. admits that he knew that she wasn't his mother even when he asked, as well as the fact that Peach displays general competence in other games at the very least (and is usually better characterized in the spin-off games, notably in the Mario RPGs).
Yoshi in general feels very tacked on; his controls are awkward, his powers are very limited, and he has Super Drowning Skills. There is, naturally, a sequence which requires you to take a Yoshi across a gargantuan stretch of ocean by utilizing Delfino Plaza boats, which are some of the most awkward platforms in the whole game.
Also, if you finish a race with Il Piantissimo after he finishes, Mario dies.
For a game with so many beautiful water features to swim in, swimming beneath the surface with finesse is a lot more difficult than it was in Super Mario 64. The underwater secrets take this to the extreme.
FLUDD is hated itself. Though, most of the hate stems not from being hard to control, but for putting the focus away from jumping, replacing the long jump (and making the backflip a minor Guide Dang It), and replacing Mario's punches.
The boat in Corona Mountain, with its very unintuitive and finicky controls and One-Hit-Point Wonder constitution.
The Pachinko Game's lock on Mario's controls is extremely vexing.
So Bad, It's Good: Many elements of the story get this reaction. Some standouts include Peach's Never Live It Down moment and anything that Bowser says. The gameplay, while controversial, fares much better.
The way you kill the Bloopers in Ricco Harbor is by ripping off their tentacles. Which then proceed to twitch violently after they're pulled off. Gooper Blooper's boss battle allows you to rip off all four of his tentacles and then yank on his cork-plugged mouth.
Petey Pirahna barfing up goop (like the other goop-Pirahnas). Which looks just like barf too.
Bowser Jr. thinks Princess Peach is his mother. She does not deny this in any way. Make of that what you will.
Stop Helping Me!: FLUDD will frequently interrupt you to give extremely obvious advice. The best example is when you're fighting Gooper Blooper, when he'll tell you what to do even if you're already doing that very thing.
Take That, Scrappy!: Talking to some Piantas will reveal that Il Piantissimo is just as unpopular to them as he is to the player. They refer to him as "rogue", "creep", "uncool", "inconsiderate" and are very insulted by his pianta costume.
The Tetris Effect: Try playing (and FAILING) at "Red Coins on the Water" (at Ricco Harbor) enough times, and you might start to see your own vision feeling like it's careening left and right the way the Surfing Blooper does if you're not gentle enough with the analog stick. This effect may persist even after you turn the game off and walk away.
Corona Mountain. The boat segment is one of the most difficult in the game. The trick to controlling the boat is this: if you're standing at the front and shoot left, it will turn right (and vice versa). If you're standing at the back and shoot left, it will turn left. If you're standing at the center of the boat and shoot left, it won't turn very much.
"The Goopy Inferno". You have no access to FLUDD until the end of the level, and the entire town is covered in flaming goop. One touch of the stuff and it's almost a nerve-wrecked mess for you.
In "The Watermelon Festival" in Gelato Beach, you have to guide a gigantic watermelon down a cliff and along a beach past a horde of Cataquacks, who, if they get anywhere close, will knock the watermelon into the air, popping it. Oh, and the controls for guiding said watermelon are hellishly awkward, and the melon itself is ridiculously fragile, causing you more often than not to make it go sideways or accidentally pop it while trying to push it. You can squirt the Cataquacks with FLUDD to stun them, but the area is so swarmed with them that for every one you can fend off, there are always two or three more coming at you from the other side. You can kill the Cataquacks beforehand with the Dune Buds or luring them into the ocean, though, making this a little easier.
"Yoshi's Fruit Adventure", where you have to squirt juice onto jumping fish to reach a series of platforms, is so frustrating that one online FAQ simply states, "I dunno, haven't finished this level."
Lily Pad Ride. One of the most frustrating mini-levels to complete. Actually getting there is annoying enough: you have to jump on a series of slow-moving boats in order to reach a small, isolated island with Yoshi, so as to remove the barrier that's blocking your way. This is already hard by itself, because Yoshi dies if he falls into the water, the boats are small, and it can be easy to miss a jump. The level itself, however, is even worse. You have to ride on a slowly-sinking lily pad in order to collect eight Red Coins, so you can obtain the Shine. The water kills you instantly, and the currents are too fast for you to backtrack, meaning that not only is it very easy to miss a coin, but if you do, you're screwed.note You can return to the start of the level without dying or leaving the level. However, it requires patience and a steady hand. Just walk along the narrow edge of the level. It's a long trip, and it's easy to fall, but it is doable. Prepare a lot of extra lives, because this is hard. One last thing: do not assume the Warp Pipe at the end is a nice and convenient way to return to the start of the level. It sends you back to Delfino Plaza.
Any of the FLUDD-less platforming levels, to the point where just hearing "Platforms-A-Plenty!" is enough to make players start frothing at the mouth in rage. And you have to visit these places twice: First time to just conquer the course and get the Shine and the second time (with your FLUDD this time) in order to complete a red coin challenge for a secret Shine. The red coin challenges are even nastier due to having to do things you wouldn't have done on the first go-around and they're a Timed Mission.
Pachinko Game. You are in a pinball machine-like stage, where you need to maneuver Mario to collect eight Red Coins. The difficulty comes from one single thing: the "launcher" that propels Mario into the machine makes him go so fast, it's insanely hard to get him to land where you want to. He even goes too fast for you to use FLUDD to correct any mistakes unless you somehow touch one of the openings of the machine and don't get knocked down to your doom. Even if you collect all coins, you still need to get back into the machine to actually get the Shine. What also doesn't help is that if you skip the launcher by wall kicking up and out, you get flung to the right anyway for some undefined reason.
"The Red Coin Fish", in Noki Bay, which requires you to catch 8 red coins swimming in the shape of a giant fish. The underwater controls are highly unmaneuverable, it's extremely difficult to tell where Mario is in relation to the coins, the coins are constantly moving, and just to add insult to injury, the coins comprising the fish's body will regularly scatter outward for several seconds, leaving you with nothing to do but wait while you slowly drown.
Any of the 100 coin missions except in Pinna Park (which has two episodes where it's possible to earn 999 coins). In the predecessor, Super Mario 64, the levels were still the same (barring few exceptions) that allowed the player to collect the 100 coins needed for the star in any order and the blue coins gave the player five to help with the collection. In Sunshine, the blue coins are their own currency, so the player has to hunt down 100 coins on their own; which is a colossal pain in the ass to hunt down each and every coin possible. To compound this, only a particular mission or two in each stage will be able to give Mario the 100 coin shine, as some missions won't have 100 coins to collect; so it's easy for the player to pick the wrong mission and waste a lot of his/her time. Which mission has it? The game doesn't tell you.
This game has very few enemies and items in common with the other games in the series. Also, many fans disliked the removal of the long jump, one of Mario's best moves.
The voice acting was also heavily criticized for its generally poor quality, to the point that it was completely removed from Super Mario Galaxy, going back to basic grunts.
They Wasted a Perfectly Good Character: Poor Peach. When first we see her in the game's opening, she is the first to notice Shadow Mario running amok in Isle Delfino—twice! Once in a plane advertisement, and again at Delfino Airstrip. Because of this, she and the Toads are the only people to know for a fact that Mario is innocent. But the Piantas don't see it that way, and immediately overrule her when she tries to object on her hero's behalf. You guys know she's royalty, right? To make matters worse, just when it feels like we're going to have a grand Mario adventure WITHOUT her getting kidnapped, the first thing Shadow Mario does when he finally reveals himself is kidnap her. As a final kick in the teeth, once rescued, Peach will hang around Isle Delfino and you can even talk to her, once again making you think they're giving her a break. But no. Once you get enough Shine Sprites, she is held captive for the rest of the game, even when you start the game again after defeating Bowser for the final time. So much for a Hero of Another Story.
They Wasted a Perfectly Good Plot: The flood radically alters the layout of the hub town by putting 3/4ths of it underwater. Swimming around town is pretty neat... until you realize that you can't really do anything new with this change, and there are no significant secrets to be found. Plus, the flood inexplicably goes away on its own while you're in the final level, or if you manage to collect one of Delfino Plaza's Shine Sprites.
Visual Effects of Awesome: Sunshine is one of the best looking games ever released for the Nintendo GameCube, and Nintendo fired all cylinders on the polished, fluidly animated, and beautifully lit CGI and lush tropical environments — its graphics are so ambitious and look so good, it can still easily hold its own against contemporary video games. It says a lot that a 128-bit video game from 2002 is still regarded as having some of the best water effects in the medium.
The Woobie: Believe it or not, Mario. He's framed by Bowser Jr. for stealing Shine Sprites and graffiti and the Piantas jerkishly lock him up when he arrives. Not only do they not listen to his allies telling the truth that he did not commit the crimes, he's forced into cleaning the whole mess up, with Peach getting kidnapped again and getting visibly depressed over FLUDD's Disney Death. Thankfully, he finally gets his vacation at the end.