Pokémon themselves, and the practice of battling. Are they fully sapient Proud Warrior Race Guys engaging in their version of UFC with "coaches" who've earned their respect? Or are they little more than powerful animals being made to suffer through a sterilized depiction of cockfighting? Consider the real world equivalent of Pokémon battles, where human trainers force animals to fight for them? Bear-baiting, Cock-fighting and Dog-fighting! Yeah, it's suddenly become a lot harder to root for our heroes. The alternative to this comes when material for the series tries to characterize the Pokémon themselves beyond doing whatever their trainer tells them to, by saying all the fighting is just as much a game for them as it is for anyone playing the games. This is essentially a world which humanity shares with over eight hundred different species of super-powered Blood Knights. Considering how it's considered dangerously unsafe to walk in tall grass without a Pokémon of your own, and even a few generations later, Professor Birch gets chased by a wild dog pretty easily, this seems to actually be the case.
The Pokémon Cubone wears a skull on its head from its dead mother. One popular interpretation is that it's an orphaned baby Kangaskhan that, because of the skull, evolves into Marowak instead of Kangaskhan, though how seriously this is believed depends on the person.
Another theory is that the Ghost Pokémon Gengar is a dead Clefable because of their similar body shapes.
Less morbid is the theory that the fossil Pokémon Kabutops is an evolutionary ancestor of Scyther because they both have blade arms.
Darkrai is often depicted in canon media as dangerous and shady, and sometimes all the way up to utter monster. A common fandom alternative, though, is that it is no more malevolent than any other given Legendary and suffers from Bad Powers, Good People, requiring withdrawal from people to prevent causing pain and making itself genuinely hated. This interpretation is also confirmed to be canon in the core games, with Power Incontinence on top of the harmful nature of Darkrai's powers.
A lot of Pokémon species get this in Pokémon Ultra Sun and Ultra Moon's Pokédex entries, which are full of calling out undeserved reputations and inconsistencies. Just some examples:
Electabuzz is ostensibly responsible for nearly half of all known blackouts, but USUM claims it's being misblamed and scapegoated to cover for faults with the power companies.
Absol has classically been a walking Cassandra Truth and Chronic Hero Syndrome, but Ultra Sun sternly points out that one should be grateful for its altruism and popularity is rising in the younger generations.
Hypno, which, thanks to an old Pokédex entry, has become a shorthand for Memetic Molester, is commonly used by doctors as therapy for patients who have trouble sleeping.
Due to the sparse details provided by the games, the Pokémon themselves are subject to this in the games. They display little personality outside of Pokémon-Amie, natures, and characteristics, and their 8-bit cries would be fairly implausible to produce in a "real" setting, with their text cries alternating between Pokémon Speak and onomatopoeia. As such, the Pokémon's cries and personalities (both individuals and the whole species) are largely left up to the viewer's imagination (and whichever Alternate Continuity they like best, be it the anime, the manga, Origins, Generations, etc.), which helps fuel the fandom's large roleplaying and fanwork community. An example of this is We Are All Pokémon Trainers, where Pokémon depiction bases are left up to the writer.
Jessie, James, and Meowth in the anime are prone to this, due to their Ineffectual Sympathetic Villain status and well-developed backstories. Depending on which section of the fandom you ask, they're one of these: A) criminals who are loved because they're so bad; B) a trio of bumbling misfits who happen to look cool; C) tragically misunderstood woobies; or D) a trio of rebels who are capable of being good but like being bad too much to do a complete HeelFace Turn. Arguments over which portrayal is most accurate can lead to much Fan Wank. That their niceness or meaness changes Depending on the Writer doesn't help. More specifically, Meowth could be just as bumbling and incompetent as the other two; he could be a smart but conflicted villain who gets constantly dragged down by his desire to be be a good guy; or he could be a mastermind with enough smarts to learn Japanese (or English, for the dub) with a completely inhuman mouth and invent all sorts of scientifically improbable devices, and who pretends he wants to replace Giovanni's Persian cat-Pokémon because it makes him look incompetent.
There's also speculation that Jessie, James, and Meowth aren't villains, but deep cover heroes using the guise of incompetence to subtly influence Ash into becoming a better Trainer, and herding him into the right places to do good. Considering their motto used to start off with "To protect the world from devastation", this doesn't seem all that farfetch'd.
Then there's the fact that they're still under the employment of Giovanni and are apparently elite enough to be in personal contact with him and his assistant despite being grossly incompetent and being highly fixated on obtaining one trainer's Pikachu. There's the interpretation that Giovanni lets them go to far-flung regions and encounter other evil teams to sabotage any potential competition.
Are Jessie and James Platonic Life-Partners or are they mutually in love but unwilling to take that first step?
This also applies to Cilan. His video game counterpart has no confidence when facing the player character and his anime counterpart is rather loud in comparison. Additionally, his anime counterpart is driven farther with what Burgundy states about him and how in her Imagine Spot, she suffered a humiliating defeat from him and he taunts her. She is already made out to be a liar in the episode but when she challenges him later on in this episode, the audience sees Cilan enjoying toying with her needlessly when it would only take one hit to KO both of her Pokemon. Somehow, the idea of him being a nice guy in both continuities is shattered if you put this into perspective. This makes the idea of Cilan secretly being a bad guy and being one of the three members of the Shadow Triad more likely.
It's a never ending debate on whether Paul is either a Domestic Abuser who tortures Pokemon, never shows any care for them whatsoever, and deserves to have his license as a trainer taken away, or if he's simply a Jerk with a Heart of Jerk and very strict trainer who's also fair enough to his Pokemon and knows his methods will pay off in the end. If you look at the way Paul is from his first appearances to his last, you'll most certainly see he's made some changes.
Does Ash really keep losing league matches, or is he intentionally throwing them so he has an excuse to keep traveling?
Ash himself has gone through several phases of characterization Depending on the Writer, ranging from rookie to mentor and back again.
Some people consider him a "what-not-to-do" avatar for younger Pokémon fans for much of the series, particularly in the original and BW series. Others consider him to be a poor unfortunate soul cursed to wander endlessly without ever realizing it.
Ash's personality in Sun and Moon could be due to how one acts on vacation, especially given that he still shows extensive competence in battle.
Other fans believe Ash is utterly irresponsible trainer, dumping his Pokémon off at Oak's is especially contentious, especially with fans of said Pokémon. They view Ash's actions as a non-lethal You Have Failed Me for not winning the league. Defenders of this policy will, however, point to the issues Ash had when he did not start over his team in Johto (the comparative weakness of the Johto mons), and the additional skills the Pokemon at Oak's ranch learn being a benefit of their stay, such as Noctowl's much improved performance at the Sinnoh League, as well as the general view that Oak's ranch is a much better way of retaining his old Pokemon than the releasing and handing them off for training that Ash was prone to doing in the original series. It should also be noted that as a Merchandise-Driven show, the anime is required to showcase Ash using the newest Pokémon of every generation.
Smiling off his Kalos League loss is seen as either a sign of his apathy for his journey, avoiding to show his disappointment after the reprimand his first time in that position (post Indigo) got him, or a sign of maturity after the development he's gone through after several regions and the Ash-Greninja arc.
Ritchie as the physical representation of Ash's potential when not weighed down by his negative attributes and the Status Quo Is God constraints of a cartoon Long Runner is a popular interpretation of him...usually held by the people who don't hate his guts.
Cameron could be considered the Antithesis of Ritchie. A league rival who represents Ash's negative qualities (dopiness and impulsiveness) but amplified.
Is Charizard a lazy, freeloading, ungrateful jerk or does the lizard see Ash as unworthy to lend his strength, explaining his refusal to listen to Ash unless properly motivated before Character Development kicked in? Or alternatively, did Charizard not listen to Ash because he didn't have the right gym badges?
Something about Reggie making Paul's Electabuzz afraid of him is popular for interpretation.
Is Johanna (Dawn's mom) a pageant mom, conditioning Dawn into contests and making her succeed so she can live through her achievements, or is she honestly supporting her daughter's interest in contests after having a successful career in the field herself?
Since not much is known about Trip, it's become a fandom thing to make Trip have hidden depths that were never touched on in the anime. The most common interpretation is that Trip is secretly cute and psycho (owing to his insistence on using violent force regardless of the Venipede's potential innocence and sabotaging the peace efforts, and even after dropping the insults and awkwardly befriending Ash, he goes quickly from looking upset to face off against Ash so soon into the league to having Serperior strangle Pikachu into unconsciousness while smirking and is even blushing in the freeze frame) and is obsessed with the occult (given he has two ghost Pokémon in his party). Additionally, there are speculations that Trip actually isn't that good with battling and the reason he loses in the first round of most tournaments because he's either letting his ego get to him or he honestly is that weakand given he loses to Ash in the first round of the Unova League makes it seem like Trip isn't up to snuff like the other rivals.
It might be possible that in "Bulbasaur's Mysterious Garden" Ash's Bulbasaur didn't want to evolve because he was worried that it would suddenly become disobedient like Charmander did upon evolving into Charmeleon.
Croagunk as a Crazy Jealous Guy for Brock; for one thing, there's how their friendship is rated at the same level as that of Ash and Pikachu, even though Croagunk was just recently captured at the time the rating was made...
The Running Gag of Bianca running in, colliding with Ash, and sending him flying into a conveniently-placed body of water. Is Bianca genuinely clumsy, or is she doing it on purpose so she can have an excuse to see Ash with his shirt off?
Many, many people have pointed out that in Episode 5 of the Sun & Moon season, when Harper and Sara ask Lana if Ash is her boyfriend, Lana's first reaction is to blush and quickly deny it. A lot of people quickly started shipping the two together.
Likewise, some have interpreted Lillie's interactions with Ash in a similar way, especially her Luminescent Blush from being complimented by him in Episode 8.
Sometimes, Clemont's eyes get obscured via Scary Shiny Glasses when he tries to reprimand Bonnie on trying to hook him up with a girl, making it look like he's only pretending to be embarrassed by his sister's antics, and in reality he actually wants to find a girlfriend. And how did he find this logical? He saw Ash as an example.
Is Serena really in love with Ash, or is she love with her idealized image of him? If the latter, did it ever change into the former as the series went on?
Does Miette actually like Ash, or does she just pretend to as a way of taunting Serena?
Is Lillie truly a nice and sweet girl with a tragic past doing her best to move forward, in spite of her trauma, and gaining courage to face the future? Or is she an ungrateful spoiled brat that disliked her mother for petty reasons and never formally apologized for her behavior, while never bothering to try to understand and heal from her trauma until other people solved her problems for her?
Does Harley hate May because she called his Cacturne scary, called his cookies not half bad, had some random girl that look jist like May steal his favorite snacky, narcissistic problems, or all of the above? Quite frankly, everything about Harley seems to be up to interpretation, and no two people see him the same way.
The divisive Pokémon: I Choose You! Pikachu speaking scene has several interpretations used by fans: is it their bond finally reaching a similar state as mentioned in the main series where Ash can generally pick up on what his Pokemon mean, if not their exact choice of words? Is Ash hallucinating as a result of severe injuries, as the scene itself is blurry? Was it exactly as it seems on the surface?
Are Sapphire and Ruby really a tomboy and Camp Straight or are they hiding their true personalites?
In fandom, the Nuzlocke Challenge. You can only catch the first Pokémon you encounter in an area, and anytime a Pokémon faints, it is "dead" and must be released. How would this look to the actual in-game world? A trainer claims to love his Pokémon, but any time one of them faints, he sends it away because it's dead to him.
Cyrus— is he Well-Intentioned Extremist? Even his die-hard fans will admit that his actions were evil and he had to be stopped, but was it as simple as defeating a megalomaniac? Or was there a good motive under that insanity? Giving him a Cry for the Devil backstory—which you don't discover until he's already gone from the plot—throws a wrench in the works, as does that some of his agents want to continue his organization even with the realization that Cyrus himself had gone too far.
Part of the difference seems to come from his alternate characterization in Platinum version, especially the scene where he tells the player character that he's using the other Galactic agents and LAUGHS ABOUT IT. Cyrus LAUGHING is jarring enough (and borders on completely out of character), but consider that that entire scene didn't exist in Diamond/Pearl.
To say nothing of the differing theories as to what that he meant in that scene. The theory that he planned to be the only thing that existed doesn't seem to hold water, as he talks later about others being there, including people he wouldn't logically know about. Was he testing the player character's reaction, as he seemed to be doing with his bomb threat in Celestic and his later threat that capturing/defeating Giratina would cause everything to end (which is counterproductive to his goals as if everything ended that way, he couldn't create his new universe)? Was the "lie" refering to how he had no intention of letting his subordinants rule rather than exist at all? Or is he just being his usual inscrutable self and the true meaning of it is known only to him?
It's worth noting that there is a canon where Cyrus realizes that what he had done was wrong, although we're not told the specifics of his realization. It's also the only canon where someone shows him forgiveness, and it's implied that the two are related. However, DPA-verse was for the most part written without Platinum's characterization.
Whether or not he even knows Mewtwo exists is another issue. Team Rocket was involved with Mewtwo in the anime and Pokémon Adventures, which could feed potential Atoner theories... However, it's unclear if this applies to game Giovanni was well.
Kotone/Lyra (the female protagonist in HG/SS). Both Japanese◊ and Western fandom love depicting her with a few screws loose, partially related to her Replacement Scrappy status. The Japanese version takes it up to eleven by making her NEVER change her expression. However, this is rarely used seriously.
The nurses are caring medical practitioners who you only visit when your Pokemon are badly injured but they say they "hope to see you again soon". It comes off as malicious to some.
The internet has minorly gone nuts over an interpretation that Blue's Raticate died and was buried in Pokemon Tower. Most commonly, this was as a result of his battle with Red aboard the S.S. Anne, causing him to blame Red for it and vow to become a Pokemon Master for his dead companion. Interestingly, these interpretations tend not to focus on avenging the Raticate's death by defeating Red, but rather channeling all his sorrow into becoming a better Pokemon trainer, which would make Blue one of the most mature eleven-ish-year-olds ever. It also makes for a tragicloss of innocence story, especially when Red then takes his championship (and the love of his grandfather) mere minutes after attaining it.
There is also the theory that Blue actually joined Team Rocket at some point, looking to the fact that he is often encountered in the same area as Team Rocket, and does nothing to help save Silph Co. even though he is right there in the building and certainly strong enough to defeat Giovanni.
Blue is canonically your rival because you are of similar height, age, etc. Reasons for him going from friendly to a jerk differ, such as his parents recently dying or him being jealous of you.
Red has various interpretations on both design and personality. His remake design is always shown scowling in official art and his Super Smash Bros. counterpart is a bit of a Jerkass (or at least is quite cocky) along with his Pocket Monsters counterpart, though the games imply he's a nice Determinator. But his classic design is shown both scowling and happy, smiling, friendly, and Hot-Blooded in official art. Fans love to portray him as The Stoic. Sun and Moon seems to have canonized the stoic version of Red, at least as an adult.
Furthermore, with Red's appearance as the Final Boss of Gold/Silver and the remakes, there's debate as to whether he's a Blood Knight always looking for the next battle (he's found at the end of The Very Definitely Final Dungeon which has the strongest pokemon in the game), a Retired Bad Ass that just wants to be left alone (as far from civilization as possible in game), a Death Seeker in the sense that he wants someone who can finally defeat him (see previous reasons and add that he vanishes after he's beaten), or just a kid travelling around with his Pokémon.
Colress in Pokémon Black 2 and White 2. Is it clear that he was in league with Ghetsis and the rest of Team Plasma in wanting to take over Unova with Kyurem? Or was he working with Ghetsis by force and not by habit of wanting to do such a thing? He expresses that his desire is to bring out the entirety of Pokemon potential no matter what it takes, even if the entire world is destroyed as a result. But he didn't agree with the old Team Plasma's approach of Pokemon liberation. In addition, when you approach Terrakion on Route 22, he doesn't seem concerned about the fact that you plan to confront them, and gives you the Colress Machine so you can wake up the Crustle in Seaside Cave that's blocking the path to the frigate. And after you beat him, he commends your relationship with your team and encourages you to put a stop to Ghetsis' plans. Then, after beating him in the post-game, he reveals that he detested Ghetsis from the very start, hinting that he wasn't quite in league with said plans. So what he really was out for is your call.
Then there's the fact that Ghetsis himself implies that Colress's goals conflicted with his when you meet him on the Frigate. While this seems to lean towards Colress not really being in the league with Ghetsis, what it really means is still somewhat open to interpretation.
Team Rocket Executive Ariana looks quite a bit like the HGSS rival Silver and her English name is Welsh for "Silver". Could they be related, even mother and son? If so, what is their bond like? Does Silver even know?
How bad of a parent is the Big BadLusamine from Pokémon Sun and Moon? Is her behavior due to Nihilego's toxins or not? Fans differ from her being a perfectly good parent until she became Brainwashed and Crazy, her being abusive on her own but spiraling even more out of control due to the toxins, or her being in control at all times.
There are some implications that Guzma has physically and emotionally Abusive Parents. This brings his rebellious attitude and distrust of others into a new light. It also explains why he is so dedicated to Lusamine. She's mentioned to be the only adult that respected him.
NPC trainers and the player character can easily be twisted into Jerkasses with regards to their interactions:
You're wandering down a road miles away from home, your Pokémon are weak, possibly paralyzed or poisoned, several are knocked out, you're out of healing items and are desperately looking for a Pokémon center to heal your Pokémon but don't know your way around the area. As you struggle onward another trainer spots you and immediately challenges you to a battle, giving you no chance to back down and having no regard for the safety and well-being of your 'Mons.
But then, the reverse. You see a trainer looking down the road and talk to them to challenge them to a battle. They only have one or two Pokémon five levels lower than yours, and depending on their dialogue said Pokémon may be freshly caught, or the trainer is on a losing streak, or is just out for a stroll. They may also be a young child or an old man or lady. You proceed to crush their Pokémon, take their money as spoils of victory, and leave them alone in the middle of nowhere while you continue on to find another trainer to do the same to. Your main goal in doing this is to obtain the Gym Badges and become Pokémon Champion, something which in-universe, especially in Black and White, is seen by the in-game characters as the hollow, pointless goal of pursuing power and fame just for the sake of being powerful and famous. Congratulations, you're a Sociopathic HeroVillain Protagonist! Oh and that trainer you managed to avoid on one of the first few routes? Why not fight his level 5 Bug Pokémon with a team of level 100 legendaries, bonus points if you use Mew and/or Arceus.