* AlternateCharacterInterpretation: Fans consistently debate on whether or not Guildmaster Wigglytuff's off-kilter, laid back ways are [[ObfuscatingStupidity him deliberately concealing how much he really knows]] or if he's just a GeniusDitz with moments of CrouchingMoronHiddenBadass.
* AnticlimaxBoss: Unless you're really playing with the worst possible duo to fight that boss. [[spoiler: Kubutops and the Omastar brothers]] in the Brine Cave are dramatically hyped-up in-story as "vicious Pokemon" that Chatot and Wigglytuff barely managed to ''survive'' encountering in the past. They also [[spoiler: take out Team Skull effortlessly]]. They all happen to be Rock/Water types though, so if you or the partner is a Grass type, the battle is pathetically easy. Even some Fire type starters can win the battle without much difficulty, especially if they're able to exploit the Rock type of the ennemies, for example with Fighting-type moves (Focus Punch can deal [[ForMassiveDamage massive damage]] to them, if not [[OneHitKill one-hit-kill]] the [[spoiler: Omastar brothers]].
* BigLippedAlligatorMoment: '''RANDOM LUDICOLO DANCE SEQUENCE!''' '''OHHHHH YEEAAAAAAHH!'''
* CompleteMonster: [[TheChessmaster Darkrai]] is the true BigBad, and is far more evil than [[WellIntentionedExtremist Classical Darkrai]]. He was responsible for the collapsing of Temporal Tower that lead to the BadFuture, tortures an [[WouldHurtAChild innocent child]] with [[MindRape violent nightmares]] to lure out the the PlayerCharacter and his partner, and makes several attempts to assassinate them so he can try his plans again. One of his murder attempts involves trying to get the heroes to [[DrivenToSuicide willingly commit suicide]] by tricking them into thinking their existence is threatening the space-time continuum due to TimeTravel shenanigans, which is easily one of the darkest moments in any ''Pokémon'' game. He has no regrets for his crimes and wishes nothing more than the [[OmnicidalManiac complete and utter destruction of the world]], just so he can rule the tattered remains.
* CriticalDissonance: Critics gave it a tepid-at-best reception. Fans on the other hand have given it CultClassic status for its powerful and moving story, and it is widely considered to be among the best ''Franchise/{{Pokemon}}'' spinoffs.
* CultClassic: Due mainly to its narrative and a soundtrack brimming with great music, this side-game has almost as many fans as any entry of the main ''{{Pokemon}}'' series, and it still remains a popular and well-regarded game even years after its debut--if anything, after some [[ContestedSequel Contested Sequels]] in both the main franchise and the ''Mystery Dungeon'' subseries, it's gotten ''more'' popular with time. ''[[UpdatedRerelease Sky]]'' in particular is well-regarded for adding in the Special Episodes, increasing the number of playable Pokemon, and letting players experience the soundtrack whenever they want with the Sky Jukebox.
* DemonicSpiders: Purugly in the Hidden Land. They have Fury Swipes, which is already annoying when you consider multi-strike moves are {{Game Breaker}}s, and Swagger, a confusion-inducing move that boosts your attack so you're likely to miss or hit your allies.
** Pretty much ANYTHING in Temporal Spire. Specifically, the Porygon-Z who have Discharge which will hit you no matter where you are for really high damage which you likely won't be resistant to, and use Agility to boost the speed of every enemy in the room, meaning a MightyGlacier like Salamence will now [[OhCrap hit twice as fast]]. Salamence and Metagross also hit like trucks and if you're weak to Psychic, Dragon, Steel, or Fighting, you'll die really quickly to Bullet Punch, Psychic, Dragon Claw, and Meteor Mash respectively.
* EarWorm: Aegis cave. It doesn't help that Aegis Cave is the setting for a particularly time-consuming and tedious mission.
* EvenBetterSequel: Although both ''Explorers'' and ''Rescue Team'' were received about the same by critics (that is, lukewarm), most fans agree that ''Explorers'' has a better storyline and character development. The fact that the bond between you and your partner doesn't dissolve after the credits play helps a lot too.
* FanPreferredCouple: The player character and the partner, even if they're both [[HoYay the same sex]].
** [[HoYay Wigglytuff and Chatot]].
* FridgeLogic: In a world where the sun never shines, the water doesn't flow and the seasons are non-existent, how do the native Pokemon stay alive when their food sources are frozen in time and thus can't grow anything?
** Maybe Celebi uses the Passage of Time to travel to the past and get whatever food and water they need.
** Apples, berries, and seeds randomly generate in the future dungeons just as well as they do in the past dungeons. Whether or not this is some kind of weird GameplayAndStorySegregation may be up to interpretation, though.
** The randomly generated food in dungeons would give inhabitants of the BadFuture some things to eat, but since food still isn't quite plentiful, it's very likely that starvation is an issue for many Pokemon. Notice that in the dungeons in the future, nearly 1/3 of the encountered enemy species are [[FridgeHorror Ghost-type...]]
*** Bonus points go to Spiritomb for being [[ManySpiritsInsideOfOne a fusion of 108 deceased people/Pokémon souls]].
* GoodBadBugs: Occasionally, when winning big at the Recycle Shop, the prize is a higher tier ticket. You can receive and redeem it even if the shop doesn't offer the tier yet.
* HesJustHiding: A fair portion of the fandom's reaction to [[spoiler:Grovyle's]] disappearance near the end of the main arc. What actually happened to him was later revealed in Special Episode 5 of ''Explorers of Sky''.
* HilariousInHindsight: Wigglytuff proves his CrouchingMoronHiddenBadass credentials by defeating Team Skull in an offscreen battle. It becomes even more impressive as of ''VideoGame/PokemonXAndY'', which makes Wigglytuff a Fairy-type and thus particularly weak against the Poison-type attacks that constitute Team Skull's primary offense.
** In ''Sky'', most evolutionary families get a 3-star exclusive item that, when in the inventory, has the Pokemon healed by damaging moves of a certain type, instead of taking damage. Said type is usually one that would deal super effective damage otherwise, but there are exceptions. One of such is the Bronzor evolutionary family, who get healed by Ghost-type moves, which dealt neutral damage to them. Fast-forward into Generation VI, and now Bronzor and Bronzong are indeed weak to Ghost-type moves thanks to the changes in the type chart.
%%* MagnificentBastard: [[spoiler: Dusknoir]] and Darkrai certainly qualify.
* MemeticMolester:
** Drowzee was this in the main series thanks to its Pokédex entries; the mission where you have to rescue a child from him only escalated his status as one.
** According to Bidoof's Diary, Croagunk sneaks into the men's bedroom and watches Bidoof sleep while smiling creepily.
* NeverLiveItDown: "Perfect Apple Incident" anyone?
* ParanoiaFuel: In Time/Darkness/Sky, a conversation with your partner about [[spoiler: killing yourselves]] ends abruptly as the two of you go to sleep. When you wake up, [[spoiler:your partner's bed is ''empty''.]]
* PlayerPunch: The ending of Special Episode 2 in ''Sky''- ''Igglybuff the Prodigy''. Igglybuff has befriended his loyal, trustworthy master (a retired explorer), they've explored and found heaps of treasure. Then, after they beat a remote dungeon, Igglybuff's friends and parents turn up to reveal that [[spoiler: Igglybuff's mentor, Armaldo, is actually a B-rank outlaw. You can practically see Igglybuff's world ending as Armaldo's taken into police custody.]]
* RescuedFromTheScrappyHeap: Most of Chatot's detractors (especially over the Perfect Apple incident) were rather impressed by his actions in the Brine Cave.
* TheScrappy:
** [=PMD2's=] Chatot. Of course. In a way, he's [[CrossesTheLineTwice irritating to the point of actually being humorous]].
** Cresselia as well. More for being a LeeroyJenkins EscortMission in what's already a candidate for ThatOneLevel and against ThatOneBoss.
* ScrappyLevel: Who in the hell thought the Aegis Cave challenge was a good idea? At some point in the after the end, your team will be required to go to a dungeon called Aegis Cave. To get through, you must solve three word puzzles by spelling out ICE, STEEL, and ROCK. In order to do this, you must go through each dungeon and fight multiple Unown who might drop a corresponding letter stone for you to spell these words with. ''Might''. You will inevitably have to go through each of these dungeons multiple times to get the correct letters. And this challenge is mandatory.
** Best part? If you want to go back to recruit the legendary golems, you have to spell out the words all over again. And you might not even recruit them on the first try.
** However, you can use the Wondermail Generator to get codes for jobs that will get these items. It's still annoying, but better then what you have to do otherwise.
* SequelDisplacement: While not as bad as some examples of this trope, some believe that Explorers of Time/Darkness/Sky were the originals and don't know about Red/Blue Rescue Team or just ignore it.
* TearJerker: [[spoiler: The ending cutscene. ''All of it''. Your character disappears before your partner's eyes, leaving them staggering towards the Rainbow Stoneship alone. Several months later, they find themselves on the very beach where they first met you...and end up ''breaking down in tears'' after remembering all the adventures you had.]]
* ThatOneBoss: Palkia can be troublesome too, if he feels like spamming Spacial Rend. It also hits the whole party, and unlike Dialga's Roar of Time, he doesn't have to spend a turn recharging.
** Dialga can count too. though he has the turn-recharging drawback, it hardly comes into play if his Roar of Time can ''outright'' kill either one or all of your party members at full health.
* ThatOneLevel:
** Temporal Spire from the second game may perhaps hold one of the most punishing [[DifficultySpike difficulty]] spikes in recent years thanks to a myriad of reasons. The penultimate stage of the main story only allows you and your partner in, meaning if either one of the two are any sort of weak to the many traps and strong Pokemon in the dungeon, then [[ForcedLevelGrinding grinding]] for experience or for items will be the norm until a winning combination has been made.
*** The real reason for its notorious nature comes from the enemies, '''all of which qualify as a [[DemonicSpiders Demonic Spider]] in one way or another.''' Porygon2 and Porygon-Z will boost every enemy's Speed in a room with Agility and hit you or your partner from virtually anywhere with Discharge, Tri Attack and Signal Beam. Bronzong, thanks to the game's mechanics, is a Pokemon with no real weakness and its defenses allow other enemies to ambush you during the fight with one. Salamence and Metagross both will martyr everything in their paths with Dragon Claw and Meteor Mash, respectively, severely damaging, if not outright knocking you or your partner out. Combine that with Monster Houses and the littered traps, and the spire's infamy has since risen to a plane that even rivals Stage 6 of [[VideoGame/NinjaGaiden Ninja Gaiden]].
** Any of the Legendary dungeons in the second game, i.e. Bottomless Ocean, Giant Volcano, etc.
** Mt. Bristle can be a bit of a challenge for the sole reason that you're not quite strong yet. Like the EarlyBirdBoss, but for a level instead.
*** Not helped by the fact that Drowzee might be a bit of an EarlyBirdBoss, if you get unlucky and his Forewarn ability activates a lot.
* TierInducedScrappy: Cresselia in ''Explorers Of Time/Darkness/Sky'' is perhaps the worst when it comes to this. Not only do you have to escort her to the end of the dungeon (Which contains tons and tons of lava for her to float over and burn herself with), but she also takes place in the final battle against [[spoiler:Darkrai]].
*** That being said, she at least has the Lava Evader IQ Skill, so she won't go onto the lava on her own.
%%* ToughActToFollow: ''VideoGame/PokemonMysteryDungeonGatesToInfinity'' was always going to have a hard time coming after this one.
* TheyWastedAPerfectlyGoodCharacter: The role of Giratina. You would think that [[spoiler: Giratina would be the game's TrueFinalBoss, what with being the Pokemon stronger than both Dialga and Palkia, as well as a rival and enemy of Dialga, Palkia, and Arceus.]] Obviously, if the game were to have a greater villain, Giratina would be the one, right? Nope, [[spoiler: Giratina is a mere treasure-guarder, while Darkrai, a lesser legendary with the same stat total as Goodra, no relation to Dialga/Palkia/Arceus, and no plausible way to overpower the likes of Dialga is the TrueFinalBoss.]]
* WhatAnIdiot: Yet again, the 'Perfect Apple' incident. Thanks Chatot, [[SarcasmMode your insight and actions on the whole incident were really appreciated]].
* WhatDoYouMeanItsForKids: You learn at the end of the game [[spoiler: that you are essentially on a suicide mission.]]
* TheWoobie:
** Bidoof, especially seen in his special episode.
** [[spoiler: The partner, after the player disappears. Or him/her in general? For one, s/he's a young Pokemon (presumably a kid) who's also a coward who only got the strength to join the guild from the player, s/he's gone without dinner because of Team Skull, they were bullied by Team Skull in general, and their best friend/life partner disappears into light before their eyes, leaving them to go home alone while barely being able to hold themselves together. Things seem to be looking up for them when they return, only to have Cresselia (actually Darkrai in disguise) tells them to kill themselves along with the player because they are an anomaly. Ouch.]]
** What about The Player himself/herself? For starters, they're an amnesiac [[spoiler: from the future]] who has lost their family and turned into a Pokemon. [[spoiler: Especially when finding out he/she exists only because of a bad future and they'll disappear once Primal Dialga is defeated. Pretty much ''everyone'' from the BadFuture could qualify, except the Sableye and Dusknoir. Grovyle for being an idealist who wants to change the past even if it means he won't exist, Celebi for using most of her energy to send Grovyle, The player, and your partner to the present day and risking being murdered by Dusknoir's Sableye. It only gets worse after the post game story where Cresselia (actually Darkrai) asks you and your partner to kill yourselves to save the world, you're hunted by a well-meaning Palkia, and nearly killed by Darkrai in a nightmare when you dare to interfere with his plans.]] Manaphy could also qualify being a baby who ended up living away from his adoptive parents (you and the partner), and missing the sea despite the fact he enjoys being with you.