These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Crowning Music of Awesome: Created by Arata Iiyoshi (aka S.D.D.) & Atsuhiro Ishizuna, each series has many memorable tracks reprising several distinct melodies and themes. Explorers of Sky eventually unlocks a Sound Test where the player can listen to the entire soundtrack (all 141 songs!) at their leisure. Among the picks:
The music that plays in Crystal Cave (Tracks #43 and #44). If crystals could be played like musical instruments, they'd sound like that.
How about Track #59, "Hidden Highland"? It makes a nice dungeon theme, but it is truly memorable for its use during the scenes when Dusknoir warns about being erased from history, and again during Grovyle's special episode for Dusknoir's Hannibal Lecture, and Darkrai's Motive Rant at the end of the epilogue story.
Track #62, "Through the Sea of Time": First heard during the player's entry into the Hidden Land, this piece takes on a new meaning when it emotionally punctuates Grovyle's Heroic Sacrifice against Dusknoir. Track #63, "In the Hands of Fate", which reprises the same melody slowly and solo, is also heard a precious few times.
Tracks #70 and #72, "Don't Ever Forget..." and "Farther Away...", could be the single most emotional theme in the entire soundtrack, considering that it's heard only after defeating the Final Boss, right as the change in history erases the player from existence, leaving the partner to return home alone.
Demonic Spiders: Pokémon with multi-hit moves in general. Octillery is probably the best individual example of the trope—it packs Bullet Seed, which hits multiple times from a distance, among other things.
Any enemy with moves that hit an entire room. Nidoqueen with Earth Power and Ledian with Silver Wind WILL make you tear your hair out.
8.8: The fans were not happy about some review scores, particularly the 3/10 Game Informer gave Blue Rescue Team.
Unlike the main Pokémon series, "movement speed" actually provides a Haste effect, giving the user multiple turns in a row. It wears off quickly, but a quickened Pokémon can inflict a lot of damage if they also know attacks capable of hitting an entire room. This goes double in Monster Houses, where an enemy Pokémon using "Agility" can increase all enemies to double/triple/quadruple turns.
Due to the lack of genders in the original games, Attract could effectively disable anything in Red and Blue for several turns, even bosses.
Multi-Hit attacks (Bullet Seed, Fury Swipes/Attack, Pin Missile). Due to the damage calculation in the Mystery Dungeon games being much different than the mainstream titles, these moves now hit as hard as most other attacks each individual hit. This is made worse for the fact that the STAB bonus from the mainstream titles is also implemented in the Mystery Dungeon games, meaning with the right Pokémon (A Treecko with Bullet Seed and the Concentrator skill for instance), this can be quite lethal.
Petrify or Foe-Seal Orbs render Monster Houses pretty much trivial: they freeze every enemy in the room until attacked, letting you mop them up one by one and gather the sweet loot. What's more, your A.I. team is smart enough not to attack any enemy under the effect, so you don't have to worry about them ruining it and dooming you.
Goddamned Bats: Pretty much anything that can inflict Poison status, attack from a distance (most Water-type attacks have ranged capability), or from within walls (the Ghost types).
Doom Seeds: You better pray that an enemy 'mon doesn't throw these at you...
Spinarak, a mon that can cause the aforementioned poison along with a slow, causing it to go twice as much as you.
Magnum Opus: The Explorers games for their story, which is considered one of the best in Nintendo history.
Nintendo Hard: Especially the bonus dungeons, some of which totally empty your inventory and level you down to 1. It's because of this that Purity Forest and Zero Isle South are many players' favorite dungeons.
Magnagate has also been hit with this since the Japanese demo was first released. For details, see its entry below.
Tier-Induced Scrappy: Pretty much anyEscort Mission you do will include this. You can't assign tactics to them if they get separated, and in Red/Blue Rescue Team the escorted Pokémon was almost always at Level 1, making it easy for enemy Pokémon to KO them. To put it nicely, these are the guys who tend to waste all your Heal Seeds and Reviver Seeds for doing annoyingly stupid things like wandering off and walking into lava/fire. Explorers was just a little bit nicer in the levels department, but your clients are still under-leveled.
Tough Act to Follow: Gates to Infinity is having a very hard time following the Explorers games, mostly for "not having a deep enough plot", and the fact that there is a lot less post-credits content compared to the other two games.
Anticlimax Boss: Mewtwo fits this trope to a T. Despite the fact that the cutscene before unlocking its dungeon makes it look like the most powerful Pokémon of all...it's only Level 40 and comes after 98 floors of powerful foes like Tyranitars, Alakazams and every form of starter. You should have no problems beating it quickly, especially given the massive amount of levels you're going to gain on the way to it.
The first game has Articuno. Sure, Zapdos and Moltres were already fairly strong, but Articuno is the first boss Pokémon to wield a move that strikes your whole party (Powder Snow) — be prepared to lose a few Reviver Seeds here, especially if one of your starters is Grass- or Ground-type.
Woe betide any who bring a team of a Fire/Grass to Moltres. Many have Rage Quit because of this boss thanks to most of its attacks being OHKOs to Grass types.
Explorers of Time/Darkness/Sky
Canon Sue: Wigglytuff has shades of this: he's an explorer prodigy, he has an exclusive power that is used only in cutscenes, that can basically work for any situation; he sometimes does somewhat questionable things or acts childishly at inappropriate times, but is basically never called out on it; he has far better intuition and understanding than most characters, and can solve puzzles and understand complicated situations right off the bat; he can withstand attacks such as Skuntank's and Koffing's noxious gas combo without a problem, even when said attacks were previously seen blowing down the player characters without a trouble; and is constantly praised, admired and revered by several characters and there is little to no-one who says a negative thing about him or calls out on his many flaws.
To be fair, any attempts to call Wigglytuff out on his behaviour are quickly silenced by Chatot due to his fear of the former's wrath (which would appear as often as a spoiled child's temper tantrum if not for Chatot) and his power. As for why the noxious gas combo doesn't work, Wigglytuff lacks a nose (unlike the Pokemon that can be chosen from to play as or have as a partner) to suffer the full effects and is able to launch an attack against his opponents due to knowing where they came from.
Paranoia Fuel: In Time/Darkness/Sky, a conversation with your partner about killing yourselves ends abruptly as the two of you go to sleep. When you wake up, your partner's bed is empty.
Player Punch: 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 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.
Rescued from the Scrappy Heap: Most of Chatot's detractors (especially over the Perfect Apple incident) were rather impressed by his actions in the Brine Cave.
Sequel Displacement: 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.
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.
If you have Riolu, you can use Copycat to send Spacial Rend straight back at him For Massive Damage, given that it's Dragon-type, Palkia's sole elemental vulnerability.
Though Riolu is only available as a starter in Sky, and you have to answer "male" on the quiz to get it. So good luck if you're playing Time or Darkness (or if you wanted one of the female-only starters).
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 Early Bird Boss, but for a level instead.
Not helped by the fact that Drowzee might be a bit of an Early Bird Boss, if you get unlucky and his Forewarn ability activates a lot.
Tier-Induced Scrappy: 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 Darkrai.
That being said, she at least has the Lava Evader IQ Skill, so she won't go onto the lava on her own.
Magnagate and the Infinite Labyrinth / Gates to Infinity:
Anticlimax Boss: For the penultimate boss of the game, Kyurem can be defeated rather quickly if you have the right things to use against him. He can hit very hard, but he's not quite as difficult as what comes after or even before him.
Contested Sequel / Tough Act to Follow: The changes made to the gameplay is garnering a lot of flak from fans, not the least of which being that it appears that only 144 out of the 649 Pokemon are available in the game, most coming from the fifth generation.
Hilarious in Hindsight: A common complaint about the ending of Rescue Team is addressed in Magnagate's Post-Game, where you can choose not to return to the Pokemon World.
Inferred Holocaust: Occurs while your team was on their very first trip to the Great Glacier. The many humans that were called to the Pokemon world by Hydregion were lured in by Munna's deceptions and viciously beaten back into returning to the human world. Emolga tells you that there were many balls of lights in the sky near post town while you were away. Those balls of light are actually defeated humans.
Individual IQ Skills were replaced with Team Skills, which are found in dungeons and automatically applied to the whole group.
There is Downloadable Content, which is the most consistent way to obtain whichever of the five Hero/Partner candiates you didn't select.
The option to play as a female character has been completely removed, as has the option for your partner to be female in the international releases. Many girls who checked out the game were not pleased with this.