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.
Author's Saving Throw - Readers of the The Subsistence were baffled by Dawn's sudden prowess with guns with most complaining that it was an Ass Pull. Then Cornova wrote The Incipience and did some minor rewriting which better explained Dawn's sudden gain of Improbable Aiming Skills
Complete Monster: Ho-oh starts off as a Well-Intentioned Extremist, wanting to make a utopia for Pokemon by only killing off Humans and trying to limit collateral damage. He goes from that to this trope once he starts engaging in things like killing Pokémon simply because they don't agree with him and destroying the environment.
Pikachu's unrestrained fight against AJ's Sandslash is one of the series' most devastating one-on-one confrontations between non-Legendary Pokémon. It's enough to terrify a whole tribe of wild Pikachu into polite diplomacy.
Magnificent Bastard: Uxie, he may be an emotionless little Complete Monster organizing a genocide For Science!, but seeing him effortlessly create masterful plots and gambits with complete nonchalance, Nerves of Steel, while treating every game changing scientific advancement and atrocity he commits like it was just a normal day of the week really has got to make you admire him. There's a reason why he's the REAL Big Bad.
Nausea Fuel - the authors sometimes get a little too detailed and graphic with the descriptions of what undampened Pokémon attacks do to living beings.
Squick - Well, considering the nature of the story....but a non-violent example is Ash's feelings for Dawn. He's fourteen, but she's ten (taken from the fact that you start your journey at ten and she just started hers)