Anticlimax Boss: Kyurem. Despite the fact that he can hit very hard with Dragon Breath, it's a two-turn move which makes it easy for you to avoid it (and your partner too unless it decides to derp around). It can also be taken down relatively quickly if you have the right moves and/or items.
The Bittercold may also qualify. Sure, it's huge and menacing and from a narrative perspective, it's pretty awesome that you're taking on a huge ice being of death by yourself. But its difficulty is almost trivialized by the fact that it can't recover health after defeating you, and defeat to it doesn't even force you to go through any dungeon portions. Is it still epic? Yes. But your victory is an inevitability, which unfortunately takes away from the epicness.
Base Breaker: Hydreigon. He's either ridiculously awesome and funny, or he's a Jerkass for bringing you to the Pokémon world, knowing that you'd have to go back.
In general, there's a lot of debate over whether Gates or Sky is the best in the series so far. Gates is usually praised for its visuals, the fact that more Pokémon than just the main charcter and partner get focused on in the main story and join you in dungeons; the removal of a lot of the more annoying features, such as hunger; and making the game generally more faster paced. Sky, however, is praised for it's more in-depth story, which is more subtle due to its Fridge Horror aspects instead of the blatant end of the world angst of Gates, having all the Pokémon up to Gen IV, having more starter Pokémon besides Pikachu, Axew, and the Unova starters, and generally having a more fleshed out supporting cast with surprisingly deep backstories thanks to the 'Special' episodes.
The inability to choose the genders of the main character and partner in the English version of the game caught some flak, being viewed by some as another "step backwards" from previous titles in this series.note Which had some genders limited to what type of Pokémon you and your partner were. For instance, in Explorers of Sky, only males could be Shinx and only females could be Vulpix, to name two. Even though the genders of the Pokémon are largely irrelevant to the storyline, the fan base was still broken over whether or not it was necessary to remove the feature (particularly since this would've been the first game that allowed international players to directly choose the genders of the main Pokémon team).
The lack of variety in starters has been complained to no end- Even the first games had the starters from Gen I-III, Pikachu, and some others like Psyduck and Machop. Explorers of Sky had 21 overall (19 for the player, and Munchlax and Meowth for partner options), so going from that to a simple 5 seems very underwhelming. The removal of the questionnaire at the start has been debated over, although many agree it's convenient to not have to constantly soft-reset to get the starter you want.
Contested Sequel: While some changes made to the gameplay were well received like the removal of the hunger mechanic and infinite-use TMs, others like the the removal of the Player Personality Quiz and the inability to complete multiple jobs in one dungeon weren't. The huge number of Pokémon missing (only 144 Pokémon are available to recruit, most of which are from Pokémon Black and White) is also a seen as a huge step down from the previous games, which had almost every Pokémon available.
Crowning Music of Awesome: The songs "Hope" and "Despair". "Despair" is a very simple tune that, while somewhat light in pitch, manages to be exactly what its title says and then some, while "Hope" is an uplifting tune that manages to sound both anticipatory and excited at once. The Final Boss music also deserves a mention.
Volcarona can use Quiver Dance to raise their stats, including doubling their speed, which gives them an extra turn. They can use it to close in your party...or just raise their stats again. Their Silver Wind attack hits you and all your allies as long as you're in the same room as Volcarona, even if you're several squares away. And Silver Wind has a chance of raising all of Volcarona's stats...including its speed, giving it an extra turn...
Klinklang can triple (!) their speed at any given moment, giving them two extra turns to wreck you with. Their Steel-type gives them ten resistances and one full immunity, and they take very little damage from physical attacks. They come packing a move to lower your special defense by two levels, and if two or more are in the same room, their Plus/Minus ability combination raises their damage output. And they can use Discharge to attack you from anywhere in the room, just like Silver Wind, only trading the chance of stat boosts for a chance of paralyzing you instead.
Everyone Is Jesus in Purgatory: Is the Bittercold threatening the world with destruction and the Voice of Life (i.e. nature) crying out against it a metaphor for climate change?
Ending Fatigue: The battle against the final boss, the Bittercold. First, there's a four minute cutscene after leaving Kyurem behind and reaching the Winds of Despair before you fight the first stage of it. Then, after the first stage, another five minutes of cutscene before the second stage. Then after beating the Bittercold's second stage, the final cutscenes along with the credits before returning to the main menu are around 36 minutes long. So that's around 45 minutes of cutscene after beating Kyurem, and that's not counting the two parts of the Bittercold.
Fake Difficulty: The Sunken Treasure minigame will make you want to throw your 3DS across the room at least once. The idea is that you tilt the 3DS to direct the Starmie. Unfortunately, this will often not go to plan due to some kind of fuckup in the 3DS — at times, the Starmie will just not move, and you'll have to practically turn the 3DS upside down to make it move, when the damn thing will move at all. And while you can press the A button to reorient it, the game does not tell you this.
The player character and the partner, as per tradition. Oddly enough, they're both canonically male, which is a first for the Mystery Dungeon games. This only applies to the versions outside of Japan; in the Japanese version you could still choose gender of the partner and the player character is referred to with gender-neutral pronouns. Why this was altered, no one knows.
Fridge Brilliance: Everyone is automatically enamored by Virizion, who really doesn't want to be popular. This makes the fact that she ends up with Emolga in end make sense considering that he was the only guy that wasn't initially infatuated with her.
Fridge Horror: In summoning a long series of humans to their world in an attempt to defeat the Bittercold, Hydreigon is basically throwing lives at his problem until it's dealt with.
Fridge Logic: Hydreigon explains that he called out to many humans and brought them all into the Pokémon world to fight the Bittercold. After Munna and co started defeating the humans and sending them back, leaving the player as the only one left, why didn't he just call out to more humans, or bring the original ones back as soon as he could?
Game Breaker: Companion Mode can be used not just to complete jobs and train recruited Pokémon, but also to raise the team rank, expand Pokémon Paradise, save up a ton of money, and hoard useful items that are lifesavers in the toughest parts of the main quest (Oran Berries, Reviver Seeds, Pure Seeds, Joy Ribbons, etc.). Those last two are possible because of items and money being automatically put into the Deposit Box upon switching back to the main story. Not to mention that, in this mode, the plot stops completely, meaning there's no time limit to doing all of this.
And, as per-usual, multi-hit moves. Possibly even more so in this game since you can increase the power and accuracy of the moves to where, at the very least, it'll always do two to three hits for around 20-40 damage each even in the early levels. Rollout is a big offender, considering Tepig learns it pretty early and the penultimate final boss is weak to it.
Excadrill. Step one: Swords Dance. Step two: Earthquake. Step three: Everyone dies. If it's sandstorming and your Excadrill's ability is Sand Rush? Double Earthquake and double Swords Dance. Not even Flying-types are safe. The only real downside is that it's a bad idea to take other Pokémon along with one.
Goddamned Bats: Pansear. The wild ones you encounter during the Hydreigon subplot seem to be loaded with the most annoying moves possible. They have Fury Swipes, in a sub-series where multi-hit moves are Game Breakers. But even worse is Incinerate. Unlike in the main games, where it only affects held berries, here it can destroy any berry or seed in your bag. Note that the two most useful items in the game (Oran Berries and Reviver Seeds, yes, Incinerate can get rid of your Auto-Revive items) happen to be berries and seeds. They also have Yawn, which puts you to sleep, leaving you powerless to stop them burning half the contents of your bag. Oddly enough their evolved form is never anywhere near as annoying...
Liligant, also encountered during the same subplot. Their Teeter Dance move confuses your entire party unavoidably, and hits everywhere on the floor at once, meaning they don't need to be close or even within sight to use it. And given that, at the time, you have a level 64Crutch Character on your side while you're likely to be no higher than 30, confusion could very easily spell Unfriendly Fire... that will most likely be a One-Hit Kill. And Arceus help you if you don't have the Prevention Team Skill by then (which makes it so only one mon in the team is suffering a particular status ailment).
A minor case of this is Trubbish. They have a nice amount of health points and defense, meaning they won't go down easily and can throw things like Poison Gas to inflict a poison status, meaning auto-healing gets disabled. To make it worse, your are very likely to first meet them in the Glacier Palace, where you can get them with a side of hail.
Vullaby, during and after the Desolate Canyon mission. They aren't hard to beat, but they have Pluck, which does damage while stealing and eating any food a player has — randomly. If it's an Oran Berry, it'll make the fight a little harder. If it's a Cheri, Pecha or so on, then no harm really done unless the Vullaby just managed to heal itself. But all too often, a Vullaby can devour your only Reviver Seed, or one of your limited Heal Seeds. And if it's a Blast Seed...
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.
Holy Shit Quotient: Despite arguments over the games quality, many agree this game pull some of the most shocking punches in the entirety of the series so far. The crowner, by far, is Kyurem Freezes Hydragion solid and shatters him! Sure, it doesn't kill him thanks to not technically being a living Pokemon in the conventional sense, but at that point, the player does know this. As a result, the common reaction to it is "Holy shit! Did they just kill someone off on screen in a POKEMON GAME!?"
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.
Gurdurr who just like Virizion, becomes a woobie when you learn his back story.
Munna, who only wanted to live in a peaceful world with her friends, but lost hope and gave into the Bittercold's eventual destruction of the world.
Moral Event Horizon/Despair Event Horizon: Kyurem's ambush on the main party was bad enough, but destroying Hydreigon and brutally assaulting the hero in front of their partners eyes completely crossed into this territory.
Nightmare Fuel: You know the beautiful lights you can see from the hillside? Do you know what they are? They're actually the remains of Kyurem's fallen victims being sent back to their own world. Keep that in mind when you look at them over the horizon next time.
That One Boss: Munna. She comes with six flunkies, outnumbering your party nearly two-to-one. Her Mooks include four Gigalith; they can resist having their HP reach 0 with their "Tough" skill, effectively making defeating them a Luck-Based Mission. Toxicroak can use Revenge to soak up damage and dish it back twofold, and Chandelure is a dedicated annoyance with status effects. The battle usually consists of Munna hanging back away from the party and spamming Calm Mind while her Mooks gang up on you. By the time you clear a few out and go for her, she's got several Calm Minds under her belt and can spam Psybeam, which hits from across the room and can confuse. With Calm Mind boosts, Psybeam can knock away anywhere from 1/2 to 2/3 of your health bar in one go. And that's not factoring that you are guaranteed to have Virizion in your party for this fight; Virizion is weak to Psychic-type moves.
That One Level: The Worldcore can come off as this if you are caught off guard. While it doesn't have the monster density other dungeons have, those same monsters just happen to be very powerful. Salamence and Chandelure can hammer you hard, Whirlipede can decimate your stash of much-needed reviver seeds and berries with Bug Bite as well as a combination of poison and Venoshock, and Munna can tank your hits as well as inflict you with sleep (yawn) or confusion (psybeam). Add that this is when there is the mysteriosity setting adding a potentially obnoxious handicap like strengthening the enemies and that only the partner can come the first time. This can spell additional trouble for those who picked Snivy as their partner given a good portion of the monsters have a hefty grass resistance.
Pretty much every dungeon from the Great Glacier to the end of the main game can count as this.
Tough Act to Follow: Debates about the game's quality aside, being the first (actual) sequel coming off of the fan favorite Explorers games meant it had some pretty big shoes to fill. It's often theorized this trope in combination with the limited amount of Pokemon is why this game is such a hot button topic in the community.
Tear Jerker: The player leaving the Pokémon world. Hearing everyone on the Frism wishing you goodbye and telling you they'll never forget you...
Dunsparce's rejection by Virizion, made especially painful if you've ever been in Dunsparce's position in real life.
Gurdurr's back story.
Seeing your partner's reaction when Kyurem destroys Hydreigon and nearly kills the hero .
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.
The Personality Quiz was removed... but like Hunger, this feature isn't really missed by everyone.
You can't befriend very many legendaries. Those who expected to befriend Lugia, Ho-Oh, Reshiram, and Zekrom were very angry about this.
The game is much shorter than its predecessor and doesn't have nearly as much of a post-game arc.
You can only do one job off your job list at a time (as opposed to Explorers and Rescue Team, where in theory you could do eight jobs at one time if you wanted to).
The partner having no known family (or at least, he doesn't remember having a family) or friends prior to meeting the main character. It's never explained what happened to his family or why he was orphaned, even in the after game. There are also a few people who believe the main characters trying to bring the player character back to their world would have made a great after game plot to the likes of past PMD games instead of it being resolved after one dungeon and then the only thing else to do afterwards is a bunch of random Legendary challenges.
Viewer Gender Confusion: Unlike the Explorers installment, Pokémon are not assigned official genders, though they are nonetheless referred to with gendered pronouns for familiarity. This includes Virizon, who is regarded as female despite her species being officially genderless.
Many were surprised to find out Emolga was male before the other characters started referring to him using male pronouns.
And then there's the animated trailer to the game, which clearly shows that the partner is female (it's a Pikachu, who has the heart-shaped tail associated with females of that species). Arceus only knows how awkward it must have been for all the people who saw that first, only to find out the partner can only ever be male in-gamenote In the international release. In the Japanese version, while you could choose the gender of the main character and partner, the dialogue referred to them with gender-neutral terms. The fact that you get to name him first before his gender is revealed doesn't help things...
Adding onto this, if you listen closely, in the background Emolga's gasp sounds clearly feminine, even though he is confirmed as male.
Visual Effects of Awesome: General opinion is that, for being a game released so early in the 3DS' life span, it really showed off what the 3DS was capable of at the time. The most notable of which is the the Rainbow of Hope. ESPECIALLY with the 3D effects on.