* 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.
* ContestedSequel: Mainly due to being very different from the previous well-loved ''SuperMario64''.
* 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]] they appear 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.
* 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.
* 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.
** [[FridgeLogic This may be because those fans didn't beat the game and find out.]]
* 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''.
** 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.
* {{Narm}}: Bowser's voice acting and dialogue makes 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 draconian enough to work, and some people consider it to be just plain ''awesome''.
** FLUDD's DisneyDeath at the end is just goofy and pointless.
* 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''. [[BreatherLevel Not that you should be losing those races, though]]...
** 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 [[spoiler:ripping off their tentacles.]]
** Petey Pirahna barfing up goop. Which looks just like barf too.
* 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 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. 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 dunebuds, 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."
** The poison canal ride thing on the lily pads that requires Yoshi to hop across a whole sequence of boats and reach a far away island in 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.
** What? No mention of "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.
* 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.
** To some, the entire game. Evil, shadowy Mario doppelganger terrorizing Isle Delfino? Awesome! What? It's just Bowser's son who we've never heard of before in disguise? Lame.
* VillainDecay: This seems to be the only game in the main series that makes 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]].