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.
Angst? What Angst?: The Pichu from Dolce Island in the aftergame are still as cheerful as ever despite their home island being vaporized.
Man: They sure don't look like they lost their home island.
Anticlimax Boss: Giant Crobat, while definitely a cool idea, is executed in a way where it is simply not difficult especially compared to its fellow Societea bosses Ditto and Regigigas. It is a sky battle, meaning that there is no rage mode, and while the player can't use any Poke Assists, it can't break the line except through attacks. This also means that its large size actually works against it, being a bigger target to only partially circle. It also has very low health and very easy to avoid attacks (Just don't get hit by those attacks).
Complete Monster: Guardian Signs gives us Purple Eyes. Before we even learn he exists, he's beaten Rand within an inch of his life and kidnapped both his wife and daughter. Later, he beats the daughter up, too. He eventually mugs the elderly Societea members, hijacks the villain's plans, makes himself immortal, pumps up Mewtwo's power higher than it should ever be, and then commands Mewtwo to finish off Dr. Edward. And when Rand takes the shot for Edward, Purple Eyes is simply amused and continues to attack anyway, even taunting Rand's daughter about it. After you beat him, he points out that the Sky Fortress is now plummeting and will wipe out all of Oblivia, before laughing. Rand's wife said that the ruins she and her daughter were captured and tortured in is the only place that gives her recurring nightmares. In the last Extra Mission, in which an enraged Arceus is passing judgment on the human race, he arrives in person. His imprisonment and constant questioning has not redeemed him, but instead turned him into a Misanthrope Supreme who no longer wishes to rule over all humans, but instead Kill All Humans. He begins preaching to Arceus that it should go through with the destruction, but to allow himself to act as its Dragon due to their similar beliefs about humans. This only enrages Arceus more.
Mewtwo is in an ancient temple. Probably placed there by Edward, but that brings up the question of how he set up that machine in such a short time...
Game Breaker - In the second game, the steel-type assist prevents targeted Pokémon from attacking. Halfway through the game, you obtain a steel-type partner Pokémon. Do the math.
Early in the third game, you can catch a Xatu. Its assist is extremely powerful, and briefly prevents the opponent from attacking. Just put it in a corner or behind an attacking Pokémon, and you've won.
Goddamned Bats - Golbats and Crobats in the caves will not leave you alone. Generally, any aggressive Pokémon that is faster than you, such as Houndoom, would qualify.
Some fights for the final mission might count, like three Gabite. They're not much as difficult as annoying, since half of the time they will run over your line (and as such, the otherwise gamebreaking Shieldon won't make it a piece of cake). Your best bet is probably to use Steel-type assist and spam the hell out of it with small balls, and then quickly encircle it before the bar drops down.
Hilarious in Hindsight: So, we had this Giant Crobat boss. Few years later, Generation VI and Mega Evolutions come.
Moral Event Horizon: The Societea cross this when they VAPORIZE Dolce Island! And where to begin with Purple Eyes...
Probably when he beats Rand and has Nema and Leanne kidnapped. And that is before we even see him for the first time.
Kincaid crosses it in Shadows when he leaves you, many Pokémon and several subordinates on a ship that will sink in four minutes.
Surprisingly Improved Sequel: Most people think that both the story and gameplay were improved in the second and third games; Shadows of Almia replaced the capture system with a friend meter (at the cost of some of the game's difficulty; hence the "most"), and Guardian Signs allowed the reuse of friend Pokémon over and over again under certain conditions as well as making Quests less tedious by allowing you to pick up Quests as you find them rather than taking them one at a time.
That One Boss: Drapion. Not only Drapion hits quite hard, but low on HP he turns red, spamming with gas cloud giving not much time where you can freely circle him. Additionally, the fight's preceeded by two Rhyhorn and three Stunky, and you have to do all three in a row. And this is before you get the handy Shieldon. Even these Drowzeenote As Drapion is classified as being Poison-type, therefore being weak to Psychic-type Assists. on the ship may not be enough of help and you may need to repeat fight.
Salamence from the original game. His attacks hurt, he has one of the highest loop count in the entire game, and making any loops is hard (since there's only that much time he's in the air and landing counts as an attack; on top of that, circling him on the ground is harder, since he has a habit of beaming you when you try to loop). Oh, and he doesn't give a damn about your partner's assist, even though he isn't immune to Electric-type.
That One Sidequest: If you consider the Past missions in Guardian Signs to be one big sidequest adventure, then it's this because of how insane several of them are, especially when playing alone.