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* AlternateCharacterInterpretation: Because of just how exaggerated the KangarooCourt 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 (and in fairness, Mario is a bit of a Trouble Magnet and is undoubtedly the reason Bowser and Jr. are there). There's also a group of Piantas in ''PaperMarioTheThousandYearDoor'' that are clearly running a crime syndicate, which does little to dissuade such interpretation (though, again in fairness, this was in [[MoreCriminalsThanTargets Rogueport]]).
* AnticlimaxBoss: Just GroundPound the platforms in the final boss's stage, which is very easy because his attacks aren't that hard to avoid.
* BadassDecay: Bowser had gone from an imposing antagonist in ''64'' to a goofy dad with an easy final boss fight. Thankfully, ''VideoGame/SuperMarioGalaxy'' rectified this.
* BrokenBase[=/=]ContestedSequel: Mainly due to being very different from the previous well-loved ''VideoGame/SuperMario64''.
* CaptainObviousAesop: 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.
* CrowningMusicOfAwesome: Some of the best tropical music in any video game. Also, [[http://www.youtube.com/watch?v=k6eYNCwTHf4 "Platforms A Plenty!"]], aka "Warp Zone Theme", AKA "Extremely Kick-Ass A Capella Rendition of the Mario Theme", AKA "The awesome theme that drives gamers mad due to the [[ThatOneLevel insanely hard levels]] it appears on".
* DemonicSpiders: 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.
* DisappointingLastLevel: Corona Mountain is rather short and empty.
* EnsembleDarkhorse: Petey Piranha made his first appearance in this game, and would appear again in ''VideoGame/MarioKart Double Dash!!'', ''VideoGame/SuperPrincessPeach'', ''SuperSmashBros Brawl'', ''VideoGame/NewSuperMarioBros'', ''VideoGame/MarioAndLuigiPartnersInTime'', ''VideoGame/PaperMarioStickerStar'', and most of the Mario Sports titles. ''VideoGame/SuperMarioGalaxy'' would feature "Dino-Piranha", an {{Expy}} of him.
* EpilepticTrees: 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 [[spoiler:the Paintbrush was an invention of Professor E. Gadd's]] has led fans to come up with many an AlternateCharacterInterpretation for him.
** That Peach had to think about it for a second [[spoiler: when Bowser Jr. said she was his mother]] got a lot of people wondering why she had to think about it.
* FanonDiscontinuity: Despite [[spoiler: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.
* FranchiseOriginalSin: This was the first 3D Mario Platformer to have Mario die if you fail a minigame. This would be carried over into [[VideoGame/SuperMarioGalaxy later]] [[VideoGame/SuperMarioGalaxy2 games]].
* GoddamnedBats:
** Swoopin' Stus, the pudding-shaped creatures that spontaneously arise out of any goop that's lying around.
** [[EverythingsWorseWithBees 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.
** 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 DemonicSpiders in the Watermelon Festival, as they'll do the same to your watermelon, destroying it and making you start over.
* HilariousInHindsight: FLUDD's Hover Nozzle feature is eerily similar to the [[http://tiwibzone.tiwib.netdna-cdn.com/images/water-jet-pack-jetlev.jpg real-life water-propelled jetpacks]] that would eventually come into being well after the game's conception.
* {{Narm}}: 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.
** NarmCharm: At the same time, Bowser's voice sounds draconic enough to work, and some people consider it to be just plain ''awesome''.
** FLUDD's DisneyDeath at the end is just goofy and pointless.
* OlderThanTheyThink: The "Bowser disrupts Mario and Peach's vacation" story angle was also done in ''SuperMarioWorld''.
* ReplacementScrappy: Bowser Jr. for the Koopalings. [[RescuedFromTheScrappyHeap Until]] ''VideoGame/NewSuperMarioBrosWii''.
* ScrappyMechanic:
** Yoshi in general feels very tacked on; his controls are awkward, his powers are very limited, and he has SuperDrowningSkills.
** FLUDD, the central gimmick of the game, 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 GuideDangIt), and replacing Mario's punches.
** 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''.
* {{Squick}}:
** 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.
** Petey Pirahna barfing up goop. Which looks just like barf too.
* StopHelpingMe: 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.
* TheTetrisEffect: Try playing (and FAILING) at "[[http://www.youtube.com/watch?v=I9gP4oV4REw 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.
* ThatOneBoss: Phantamanta in the first mission at Sirena Beach.
** The music, a somewhat darker version of the usual boss theme, doesn't help. At all.
** Eely Mouth mouth as well, mostly due to bad water controls, and you have to get very close to him to hurt him, and being that close is very dangerous as his attacks are quite tricky to dodge up close.
* ThatOneLevel: Corona Mountain. We're looking at you, annoying boat puzzle. 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. ''You''. ''Will''. ''Cry''.
** 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.[[/note]] 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 (as mentioned above in CrowningMusicOfAwesome) just hearing "Platforms-A-Plenty!" is enough to make players start frothing at the mouth in rage.
** "Mysterious Hotel Delfino". ''Plenty'' of {{Fridge Logic}} plagues the mission, like how the ''one'' single fruit that the fruit bar doesn't have is the exact one Yoshi wants and the fact the Pianta guarding the Shine Sprite will not let Mario just get it ''just'' because he's not wearing the proper swimwear. Add to that a ''lot'' of {{Guide Dang It}} moments as well as two wonky moments '''''in a row''''' and you got a mission that many gamers have come to loathe. At least, unlike most other examples of ThatOneLevel in this game, it's more annoying than infuriating, because much of the mission itself is actually easy if you know where to go.[[note]]Plus, you can use a glitch to skip the entire level and get the Shine without going through the entire hotel.[[/note]]
** 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 fuck-ups 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.
* TheyChangedItNowItSucks: This game has very few enemies and items in common with the other games in the series. Also, many fans dislike the removal of the long jump, one of Mario's best moves.
** The [[{{Narm}} voice acting]] was also heavily criticized for its generally poor quality, to the point that it was completely removed from ''SuperMarioGalaxy'', going back to basic grunts.
* {{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.
* TheUntwist: It's not until Pinna Park that you get any explicit evidence that Bowser is involved in the plot at all, but him having been the villain in all the previous ''Mario'' {{Platform Game}}s except ''VideoGame/SuperMarioBros2'' meant that nobody was really surprised when he showed up anyway.
* VillainDecay: This seems to be the only game in the main series that makes [[spoiler: Bowser]] seem goofy, instead of the {{Badass}} BigBad he usually is portrayed as in the platformers, if only for [[{{Narm}} the lousy voice acting]] and the [[AnticlimaxBoss ridiculously easy boss fight]].
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