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.
Complete Monster: Deoxys, the Big Bad. His first action after coming to earth is murdering and torturing a small Pokémon child after his twin was just murdered before his eyes. Over the course of the story, he maims, murders, slaughters, mutilates, and does everything in his power to make the heroes' lives a living and total hell. He nukes several heavily populated areas around the world with his virus to acquire more mindless minions for his goal (and every single one of his minions is in agonizing pain every second they're existing) and will do everything and anything to punish those who gets in his ways. In fact, he sums it perfectly when questioned why he does all of his atrocious acts.
Deoxys: Because it is my wish. Because they were in my way. And most importantly, because I can.
Critical Research Failure: Rock-types are NOT immune to electricity. Pikachu could have easily taken both of Latias Sr.'s Pokemon.
Deoxys crosses this when he destroys an entire city, personally striking down the Pichu Brothers.
Ford has his partner Blaziken brutally torture Charizard, and turns Ash into Alpha Ranger.
Mariah nearly destroys May's psyche during their battle with her insults.
Dark Latios torments his sister, kills their father Ho-oh, kills Lady Ho-oh by ripping out her spine and eating her body, force-feeds Latias her father's genitals(!), and then repeatedly rapes her both physically and mentally until she becomes an emotionless killing machine.
Strangled by the Red String: The relationship between Latias and the Ghost King, and by extension, Rayquaza is the most disliked aspect of the story. From the very beginning, Latias has been dreaming about marrying the Ghost King, even though she didn't even know what he looked like. Later on, she forgives the him for razing her hometown and murdering everyone in it in a childish fit of rage, all because because a hologram of Latios said they should get together. She obeys it without question, the reason given that she "just knew" the hologram was the real Latios. At the same time, the Ghost King shows no real remorse over destroying Alto Mare nor killing everyone in it; the only reason he regrets doing it is because it upset Latias. To add insult to injury, their love for one another is mostly told and not shown and Latias even marries the damn guy end of the story! Many readers were not at all satisfied with the story's explanation and especially not the tacked-on revelation that Kyogre secretly made the Ghost King do it at the very end, and consider it little more than glorified Stockholm Syndrome.
The Ghost King wants to apologize to Latias for destroying her city, killing all her friends, and ultimately traumatizing her. You'd Expect: He'd do everything Pokemonly possible not to dig himself a deeper hole. Wait for her to calm down before sending someone to speak on his behalf, since he can't leave the Realm of Mists. And maybe send a messenger who's not a Ghost-type. Also, drop the bounty on Ash's head, because killing him would just piss her off even more. Instead: He sends Shedinja, the very Pokemon who killed Latias' best friend, to hunt her down with a squadron of ghosts and capture her. Oh, and Shedinja is also a Jerkass, and would rather terrorize her for several days instead of just bringing her right to the King. Then: Once the King gets to speak to Latias when she has Mewtwo as her bodyguard, he tells her right to her face that he's going to kill Ash anyway, because he never breaks his promises.
Fearow's gimmick is that he eats other Pokemon and gets stronger from it. You'd Expect: He'd eat Latias immediately, because she's a legendary Pokemon. Instead: He tries to rape her for no reason, which delays him long enough for Pidgeot to rescue her. Then: He is later killed by Latias' New Powers as the Plot Demands - powers that could have been his, had he not screwed around.