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.
Wally for awakening a legendary and whom Took a Level in Badass. Also there are fans who wish he took Emerald's spot as the main character in the Battle Frontier.
Mimi and Zuzu, Ruby's Milotic and Swampert respectively, are also very popular.
Petashi, the Youngster/Pokemaniac cross who makes it to the Unova quarterfinals, is getting popular thanks to his adorable appearance and his awesome pants.
It only took one chapter for Rakutsu to achieve this status due to his job as a member of the International Police and his womanizing habits. Ironic, given how his game counterpart was initially received...
First Installment Wins: An official poll conducted in 2005 saw Red, the first protagonist, voted as the most popular character in the series. In second was Yellow, the second protagonist, who at the time of the poll had not made an appearance in years.
The latest human and Pokémon poll shows Red topping yet again (with Gold, Ruby, and Yellow ranking 2nd, 3rd, and 4th, respectively) , while Pika tops the poll for the Pokémon.
Flanderization: It's surprisingly common in fanfics, to render each character by their most recognizable character trait, such as Blue being flirtatious, Yellow being shy, Red being dense, Green being stoic and unemotional, and so on.
Growing the Beard: The manga really started to hit its stride in the second volume with the introduction of Blue, the expansion on Team Rockets' plans, and the first glimpse at Mewtwo. Then it really took off in the following volume with the raid on Silph Co.
The RS arc was chosen via poll to be re-released in wide-ban format. The arc whose legendaries had nature-based abilities and used them to wreak havoc on the region. Cue the horrific earthquake and tsunami that ravaged Japan right afterward. The aforementioned Tohoku Earthquake caused the publisher to postpone the release of second and third volume of wide-ban format.
When fans first saw the image of White trapped in the Nimbasa Ferris Wheel with N, there were a lot of rape jokes going around. When the following chapter came out, what N did to White is arguably one of the biggest tear jerkers in the entire series. It was even called a G-rated version of Netorare.
In the B2W2 chapter, Rakutsu states that Looker's battling skills aren't as polished as they should be. In the XY games, Looker's Croagunk apparently died during a mission.
In the Yellow arc, there's a flashback of Oak's Kangaskhan beating one of Agatha's ghosts with a Dizzy Punch, which should be a total cop out seeing how Normal moves don't affect Ghosts. Now about a decade later in the newer games, Kangaskhan is given the ability Scrappy...which allows Normal (and Fighting) attacks to hit Ghost types.
The new "critical captures" feature in Black and White games sound a lot like capture spots.
So, you dress up as a Rocket member to infiltrate their base, only to have your cover blown because your disguise was ripped off...Special did it long before the HGSS games were released.
Zapmolcuno is finished off by a Blastoise, Charizard, and Venusaur simultaneously using their strongest attacks. It's the Triple Finish!
In the GSC arc, Misty ends up fighting Suicune in a cave behind Tohjo Falls. Turns out there really is a cave there in the game canon...
Eusine's Electrode can fly around with the power of electric currents. Gen 4 introduces Magnet Rise note Interestingly, no current Dex entries at the time said anything about it being able to fly, but a future one did.
The manga started FatherlyShipping in the GSC arc. Hilariously enough, rather than having Falkner and Janine respect each other over their mutual daddy issues, the HGSS games took it into the other direction.
In Pokémon Platinum, you get the chance to purchase an insanely expensive villa and furnish it with insanely expensive furniture. Good thing that the lead character of the corresponding arc was conveniently already established to be insanely rich.
A green jewel meant to control Rayquaza...Emerald had one on his forehead before the HGSS games came up with the concept.
It took five generations for Game Freak to have the Gym Leaders more involved with the plot, have secondary jobs, and have them directly oppose the evil villainous team. It took only one for Pokespe.
Black's Munna clearing his head is a reference to the C-Gear. There is now a Munna C-Gear skin available.
In the GSC arc, some Rocket grunts fill a Spider Web with electricity. Gen 5 introduces the move Electroweb.
In the Platinum arc, Caitlin's personal Pokemon is a Gallade. As it turns out in the BW games, she is a master of psychic Pokemon.
The confirmation of the world tournament showcasing the Gym Leaders and Champions in B2W2... yup, Pokémon Special already called it in the GSC arc.
N gives his Servine to White. In Black 2 and White 2, you can catch N's Pokemon. Yeah Poke Spe already called it before the game even announced.
Being able to rent Pokemon actors in showbiz in Black 2 and White 2? Looks like the BW Agency will have a new source of revenue...
A trainer with the ability to read the minds of Pokemon tries to separate humans and Pokemon through the power of a legendary Pokemon. Now, is that Game!N, or Manga!Lance? (The sole difference is that Game!N isn't murderous about it.)
In the GSC chapter, the Masked Man, Pryce pointed out that each of the major villains wanted something for their goal. For Giovanni, it was possessions (matter), for Lance, it was a Pokemon utopia (space), and for him, it was to go back in time. Come Pokémon Diamond and Pearl with Dialga (master of time), Palkia (master of space), and Giratina (master of antimatter). This comes full circle in the HGSS chapter, where each former villain fights their respective dragon)
Kusaka and Yamamoto went to France. A month later, sixth gen announcements came out and it appears from the trailer that the new region is based on France. Whether this was coincidence or a research trip is unknown.
Most readers found Ruby scaring away a wild Salamence, an intimidating pseudo-legendary, with just a Poochyena, Ralts, and a Skitty to be a bit far-fetched. Then Gen VI came out and introduced a new Fairy type amongst a select group of Pokemon, with the Ralts/Kirlia/Gardevoir line being one of them. Fairy types are super effective against Dragon types. Salamence is a Dragon type. This scene holds much more water now.
It also helps that Skitty, while not a fairy type, is able to learn the fairy-type move Play Rough, which, for anyone who's seen X and Y trailers, can absolutely NAIL a dragon type like Salamence.
Likewise, Gold's Togepi takes down a Tyranitar and a Dragonite, both weak against its retconned Fairy type.
It is noted that Emerald's Pokemon are extremely affectionate towards him and go out of their way to please him. In two different battles, Sudowoodo barely survives an attack that should've taken it out and Sceptile breaks free of the "frozen" status on its own. Both of these instances are now possible in-game via Pokemon-Amie, which works through affection.
Hype Backlash: It's very rare, but it happens occasionally as a result of its common perception as the "official" manga or the one and only manga, and the fact that is greatly overshadows the other manga in the fandom's eyes. Of course, the reason it overshadows the other manga is that most of them never get released outside of Japan as well as not being long enough to warrant much discussion.
Adding to this, there's also the misconception that most fans make about the manga being very "dark and edgy" that gives new readers the impression of expecting a lot of death and blood and such, which is clearly not the case. And while yes, this manga does have the occasional blood and psychological scenes mixed in, it is still essentially a children's manga (at least up to Naruto or One Piece standards, maybe even less so). It's darker than the Pokemon anime and games, that's for certain, but outside of the franchise it's a decent shonen manga at best.
Red himself has also been paired with just about everyone.
Magnificent Bastard: Giovanni, who manipulated nearly every event in the first arc of the manga and can predict how a battle will turn out, what moves his opponent will make, how to counter-attack, AND the time it will take for it all to happen! (Given he's been a trainer for YEARS, and wrote THE BOOK on Ground types & his Viridian powers, though his have not been explained, it makes sense. It also makes him a poster-boy (man?) for this trope.)
Cyrus also qualifies; he's ahead of the good guys, even Cynthia, throughout most of the D/P arc.
Blue also demonstrates aspects of this, despite being a heroine; she manipulates nearly every event in the second arc by setting Yellow on her quest and telling her never to remove her hat— which she bugs with a GPS beacon and recording device. "I've been... um... using Yellow as my learning aid!" She eventually becomes a Guile Hero by the third arc.
One True Threesome: Diamond/Pearl/Platinum is notable for being pretty much canon; it is constantly said how the three of them represent the three parts that make up the perfect spirit, they all cried the first day they were separated since their journey, and the Platinum arc ends with them being surrogate parents to two baby Pokemon.
1) There's still plenty of time for her to grow into an Action Girl. After all, Yellow knew even less about Pokemon training when she started out.
2) She has a full-time job that doesn't leave her room for Pokemon training, nor does her job require it.
3) Said job involves running her own business. When she actually does decide that she needs to learn how to fight, she actually has to suspend her agency.
The Scrappy: Yellow and Emerald attract the most ire from fans. Especially the latter; the former being more of a Base Breaker.
On the Pokemon front, White's Tepig, Gigi, seems to be the most reviled Mon in the series. Many fans will probably never forgive her for ditching her trainer/employer (who is clearlt shown to be very fond of her) and then showing no concern as said trainer falls from the top of a Ferris wheel and slips into a coma. It gets worse with the revelation that White had actually saved Gigi from a situation that N had put her in.
Black's Musha has gotten this treatment too after it abandons Black because it didn't like the taste of his dreams anymore. It coming back though seems to have it Rescued from the Scrappy Heap.
It helps that it only left to get stronger in hopes of boosting Black's morale.
Shipping: There is a fandom for the shipping aspect. The shipping index applies here.
Most N/White shippers tend to have quite a bit of flak to launch at Black/White shippers, and vice-versa. A bit ironic, really, since the game-verse ship (FerrisWheelShipping) comes from the ever-famous ferris wheel scene, while in the manga, that scene is probably one of the biggest Tear Jerker moments in the series, with White losing Bubu to N and falling a good dozen feet to the ground, landing on her back/side. Unsurprisingly, said scene hasn't halted the shippers even slightly.
They Just Didn't Care: Viz's editor is apparently pretty lazy as the American release has quite a number of spelling mistakes, grammatical errors, and typos throughout the entire ongoing run. One egregious case has Crystal's Arcanine's nickname being spelled three different ways in the span of a only a few pages.
Toy Ship: The most canon romance with the Dex holders so far is Ruby/Sapphire, through a Slap-Slap-Kiss relationship. But they're only kids.
More tellingly, if two kids are willing to change themselves due to a traumatic event from long ago where they blame themselves for hurting the other, all for someone they'd just met, you do have to wonder just what drives them.
Well, Norman may appear very strict and unloving, but he obviously cares very much about his son. After all, he did sacrifice his dream of becoming a gym leader to take responsibility for Ruby's mistake - and eventually dying of because of it, although he got better
The latter in particular is Hilarious in Hindsight because HGSS games show that Giovanni was a complete asshole to his kid! He may or may not have loved his son but that doesn't change the fact that he walked out on him.
Except in this canon, that didn't happen, as Giovanni was only separated from his kid because his son was kidnapped by Pryce. Then he spent ten years trying to track him down. And while he leaves him again in the end, he does so only after knowing for sure that he's in good hands, and even encourages him to get stronger so that one day he can defeat him in battle! This version of Giovanni may still be a terrible person, but he's a great father in the areas it counts.
Viewer Gender Confusion: Thanks to his long red hair, there's hardly a reader who hasn't mistaken Silver for a girl upon seeing him for the first time. In-story, Gold mistakes Bugsy, the Azalea Town gym leader, for a girl when meeting him.
Villain Sue: Arguably Sird, who has had in a hand in pretty much everything evil since she debuted and has never been defeated in battle as of yet. Oh, and she can control peoples' minds somehow, too.
What Do You Mean, It's for Kids?: While this manga is indeed targeted towards elementary school children, its strong sense of character and continuity have several convinced that it's meant for an older crowd.
Woolseyism: Viz switching Green and Blue's names around may be this seeing as Red and Blue were the original games to come out in the US.
During GSC, Gold faces the Sprout Tower's sages. In the Japanese original, they have punny names; this is kept in Chuang Yi's version, but Viz played it for game accuracy and the pun was lost.
When the Gym Leaders are introduced during the Pokemon League, Lt. Surge is referred as "The Lightning Soldier" rather than his official game title, "The Lightning American", because we're not sure if America exists in this canon.
At the end of the GSC arc, rather than editing out the image of Gold patting Blue's butt, Viz made Gold claim it was an accident. Since Gold's face still indicates him doing it on purpose, it works by making him seem like he was making excuses for himself.
Dia and Pearl's pun-based manzai skits are different in every translation, for obvious reasons.
The Woobie: All of the kids qualify on at least one point of their stories.
Special mention to the Kalos kids, who have their hometown destroyed in the first round of their chapter.
Not to mention Mewtwo. The revelation that the Sinnoh chapters take place after HGSS (not to mention that this still hasn't been resolved as of the BW chapter) means that he's been chasing after Sird for years, probably under the belief that the Kanto Dex Holders (plus Silver) are still petrified.