Many of the flaws older fans criticize newer seasons for having — a formulaic plot, filler being common to the point of Arc Fatigue, bland and forgettable one-shot characters etc. — all had their roots in the Kanto and Orange Islands series which preceded them. These flaws were more or less forgiven since it was the first season and the formula wasn't entirely set in stone yet, and the filler wasn't packed close together and didn't make up a large portion of the series as it would in Johto. It also more frequently had episodes that explored character motivations and backstory, like "Go West, Young Meowth", making fans more forgiving towards it.
Unlike the games, the anime has always had a habit of depicting multiple legendary Pokémon existing (as opposed to being implied Single Specimen Species), as well as rarely, if ever, reusing old legendaries (the Celebi from Pokémon: Zoroark: Master of Illusions is not the same one as the one from Pokémon 4Ever, for instance). Though few complained about this, that changed with Pokémon: Genesect and the Legend Awakened and its controversial move to use a brand new Mewtwo over the well-known and popular one from The First Movie. Because Mewtwo was firmly established as a one-of-a-kind man-made Pokémonwho couldn't be replicated (and not naturally born like the aforementioned Celebi), many fans logically assumed it would be the same one from before, and thus were confused and upset when it turned out to be a completely different one from a separate, unseen experiment.
The movies tend to have "evil" legendaries as the supposed Big Bad, who are either really non-malicious monsters with the conflict coming from misunderstandings, or who pull a HeelFace Turn by the end. This all started back with Pokémon: The First Movie.* It can also be traced back to the episode "Island of the Giant Pokémon", which claimed that there was no such thing as a truly evil Pokémon. While some were disappointed, it being the first use of the trope (and Mewtwo being genuinely sympathetic, especially in the original Japanese version) let the film off. Fast forward to around the sixteenth movie, and many fans are sick of the continued lack of a truly villainous Pokémon when there are several cool and/or creepy candidates. It also doesn't help that by contrast, human villains are more plentiful, more evil and generally lacking in character.
One of the biggest criticisms of the Ash vs. Cameron battle in the Unova league is that Cameron was lucky enough to have his Riolu evolve into Lucario during the match to provide him the power boost needed to defeat the rest of Ash's team. A brief look at older episodes will show that this is not the first time someone managed to pull off a win thanks to a mid-battle evolution. Ash in particular has benefited from mid-battle evolutions multiple times throughout the series. The only reason this became such a big deal this team around was because it happened against the main character during an already controversial Pokémon League. In addition, and possibly ironic, is that Cameron didn't have the mythicals that Tobias had and his overall competence was seen as more annoying for a rival that could have the hand against him. It retrospectively made Ash losing to Tobias more reasonable in comparison. Ash losing to Tobias was like a player's weakened Metagross losing to a Heatran's Fire Blast. Ash losing to Cameron was a full-health Metagross getting hit by an Igglybuff's Metronome just happening to pull off a Fissure, made worse by the fact that Ash still made it into the Top 4 semifinals when he lost to Tobias, while his loss to Cameron left him in the Top 8, the first time he actually ranked lower than his previous tournament standing.
The Black and White series was initially rather well-received by the Western fandom when it first aired, due to its brisk pacing and the B-Plot involving Team Rocket igniting people's interest - a fact which is largely forgotten since the Ending Fatigue at the end. Fact is that many of its problems were apparent from the start - Ash was rebooted to an Idiot Hero, Cilan and Iris were divisive supporting characters, Team Rocket's narrative was a drastic change in characterisation, the Team Plasma plotline wasn't immediately launched and finally the pacing was too fast (with Ash's badge quest skimming over the larger roles of the Gym Leaders in the games). The flaws simply became more apparent once the interesting things failed to pan out in the end. Ironically, overtime the Black and White series has started to become more respected as the opposite of this trope - even though not considered good, it started many trends that were well received in the following seasons.
The conclusion of the Team Plasma arc in Black and White was criticized for being rushed, the Team going down like chumps and the Big Bad being The Unfought. However, this was also the case for all the prior villain Teams sans Team Rocket, who never even got a decisive confrontation. The difference was that the other Teams' lack of real significance wasn't dissimilar to how they were portrayed in the games, while the games' Team Plasma and Big Bad were extremely well received for their moral complexity and delectable evilness and the anime started with enough popular changes, including giving Team Plasma a proper buildup, that raised expectations and even attracted fans who've previously written off the anime. Besides falling short of those heightened expectations, their intended debut was canceled and the Team overhauled to match their portrayal in Black 2 and White 2 which stripped them of their interesting traits, and other anticipated plotlines went unfulfilled. Few doubt it was a coincidence they went out of their way to give Team Flare from the next series a far better portrayal.
Game Freak not being particularly good at Competitive Balance has been pretty obvious right from the beginning; the first Pokémon games are probably the least-balanced in the entire series (Mewtwo was literally uncounterable, Psychic and Normal were hilariously overpowered, and all but about fifteen of the original 151 were overshadowed or useless). This was seen as alright in the first generations because competitive battling and balance were nowhere near important considerations - most of the fanbase was too young to care, and the hardware was running on a Game Boy, meaning corners had to get cut somewhere. Decades later, this is far less forgivable, as Game Freak has made clear efforts with Competitive Balance in mind (nerfing some types or moves and buffing others, for instance) and hundreds of major tournaments have taken place - and yet Power Creep, Fake Balance, Purposefully Overpowered mons, and unrecognized Game Breakers continue to run rampant, to the point of multiple major tournaments seeing their top rankings being stormed by near-identical teams.
Since around the fifth generation, Game Freak has been making efforts to simplify the games and make them more friendly to new players. Initially, this was firmly welcomed, as many of the things they altered or removed (gutting and eventually removing the HM system, making EV training and breeding easier, making TMs infinitely reusable) were Scrappy Mechanics being kicked out or just general quality-of-life improvements that didn't impact the overall experience. However, this also included many things that made already-easy games significantly easier, such as boosting the EXP Share into a Game-Breaker or providing severely overpowered Pokémon for free, making it hard to get any kind of challenge out of the game unless one swore off those features entirely. Then Pokémon Let's Go, Pikachu! and Let's Go, Eevee! happened. In the name of being a Gateway Series for Go fans, removed tons of features that'd been part of the series for decades and turned the difficulty down even further, creating a massive Old Guard Versus New Blood rivalry that left the old guard with a game that felt braindead and patronizing.
A common criticism of later installments is the lack of post-game content other than a side quest or two involving revisited areas, a handful of new areas, some more Pokémon, and a buffed Elite Four. This was present in Pokémon Red and Blue, where there wasn't a post-game at all other than Cerulean Cave, which only had Mewtwo, and Pokémon Gold and Silver, where despite being able to go to Kanto, a lot of it is cut down compared to Gen I. This was excused since it was the first in the series and, in Gen II's case, had to undergo a lot of compression in order to fit the cartridges.
Some Pokémon are required to be traded to other players in order to evolve. If you don't have any friends who play Pokémon, you'll need to get another console and another game just to get them. While this concept was around since Gen I, there were only four Pokémon who evolved this way (and most of them, particularly Alakazam and Gengar, were really good Pokémon). Later generations began adding not only more Pokémon who evolve this way, but more prerequisites for such evolutions, such as holding a specific item while being traded to evolve. While the GTS (first introduced in Pokémon Diamond and Pearl) makes getting an Alakazam a non-issue (if you're not concerned about obedience), there's no guarantee that a Porygon2 received on the GTS will hold a Dubious Disc, making these even more frustrating to obtain (especially the Porygon line, which evolves through this method twice).
These games introduced roaming Legendaries, Pokémon that randomly move across the region. Should you, by chance, find one, they will run from the battle at the first opportunity. This basically forces you to spend several hours trying to find them so you can slowly whittle down their health before they run off, taking great care not to knock them out, and eventually try to catch them. Remember that as Legendaries, they have the lowest catch rate possible, and you will only get one chance to toss a ball before they run off. Having something with Mean Look will stop them from fleeing, but all three of them have Roar to make you run away instead.
Gen II started the trend of other "gimmicky" evolution methods such as a Pokémon needing a High Enough happiness meter, Pokemon only evolving depending on the time of day, and even a Pokémon that required an additional Pokemon present in the party to evolve. While they are not too obtuse in Gold & Silver, these evolution methods would grow only more un-intuitive as the series continues.
A controversial introduction was Baby Pokemon. Cuteness aside, they are often viewed as utterly irrelevant because they ultimately evolve (usually via happiness) into an already existing Pokemon, likely one that you had to breed (often with certain incenses in later generations) to get the baby in the first place. Generally, the only incentive to hatching them outside of filling the Pokedex is that they learn good moves that their evolved forms would miss out on, like Pichu learning Nasty Plot. Breeding Pokémon with baby forms for competitive use also adds an extra step as the babies are unable to breed themselves and need to evolve into a form that can, unlike other Pokémon that can breed automatically.
The ongoing trend of Pika-clonesnote Ridiculously Cuteelectric-type Pokémon with a rodent-like appearance, meant to be Expies of Series Mascot Pikachu has been something of a sore spot among fans for a while. It started back in Pokémon Gold and Silver with Pichu and Marill, neither of which stirred up much fuss; Marill was a Water-type that happened to bear a vague resemblance to Pikachu (hence the incredibly pervasive PikabluUrban Legend of Zelda), while Pichu was legitimately related to Pikachu, being its newly-introduced baby form. Pokémon Ruby and Sapphire brought in Plusle and Minun, a pair of Electric rabbits that borrowed a few elements from Pikachu's design, namely the cheek circles and unusual tail shape; despite not being all that useful in battle, they didn't ruffle too many feathers due to being designed around then-new Double Battles, as well as putting their own spin on Pkachu's design. Then Pokémon Diamond and Pearl's Pachirisu appeared with little reason to exist beyond marketability, and the similarities to Pikachu became much more blatant. Pokémon Black and White followed up with the equally-similar Emolga. Pokémon X and Y introduced yet another Pika-clone as part of the smallest batch of new Pokémon to date. Dedenne was perceived as wasting a valuable slot in the Pokédex that could have been occupied by a more interesting design, and the decision to make it part-Fairy was a less-than-stellar move for the reputation of the new type. Finally, Pokémon Sun and Moon did have a "true" Pika-clone, Togedemaru, but also introduced Mimikyu, whose entire premise was a parody of the Pika-clone, simultaneously mocking the phenomenon of making a shameless attempt to recapture Pikachu's popularity and making it an Ensemble Dark Horse.
Weather-based teams weren't very popular initially because altering weather would only last five turns, and the effects were rarely worth the time spent setting up. Then Gen III introduced Abilities like Drought and Drizzle that caused permanent weather effects, along with others like Swift Swim that doubled certain stats in certain weather conditions. However, Drought/Drizzle were exclusive to two Legendary Pokémon that were banned in most forms of competitive play, and sandstorms and hail were still hard to use. As time went on and more Pokémon, Abilities and items that took advantage of weather appeared, the Gen V metagame became dominated by weather teams and a few large Pokémon communities placed bans on certain Pokémon and combinations, if not banning weather/inducing abilities outright. Game Freaknerfed weather abilities themselves in Gen VI by limiting ability-caused weather to five turns, as a weather-altering move would do, and though Primal Kyogre/Groudon and Mega Rayquaza have permanent weather abilities, they only last as long as they're on the field. History may be repeating itself in regards to terrains (a field effect introduced in Gen VI), but thankfully none of them are permanent.
Super Rod only being available post-game. Not so bad in Gen II due to a large selection of Water Pokémon and you still can get Old/Good Rods. From Gen IV onwards this is justified that Super Rod is used to fish for Mons not native to the region, but at least lesser fishing rods can still be obtained beforehand. It wasn't until Gen V that fishing is off-limits period until you defeat the Elite Four which doesn't help that Water Pokémon is a minority in Unova. Those who wanted to use Water-types there but hate the Oshawott line will not be pleased.
Omega Ruby and Alpha Sapphire are often criticized for not really changing anything from the basic story of the original Ruby and Sapphire, yet the same can be said for the previous two remakes FireRed/LeafGreen and HeartGold/SoulSilver; despite having numerous additions to and differences from the originals, their basic plots remained the same. What made ORAS different is that it promised that the story would be re-imagined, making this much harder to ignore.
The Fire/Fighting type combination is loathed by much of the fanbase due to it being applied to three consecutive Fire-type starters from Generations III-V. The first such Pokémon, Blaziken, was (and still is) well-liked and considered a good Pokémon, as was Infernape. The inclusion of this typing was also somewhat justified by the first Gym of both Generations III and IV having a distinct advantage against Fire-types, which the Fighting type corrected. Emboar, however, is when fans began to get sick of the repetitive typing of Fire starters compared to their more varied Grass and Water compatriots, not helped by Emboar being seen as mediocre by comparison and the Fighting-type not having an advantage against the first Gym this time. Thankfully they've stopped the trend as Gen VI's fire starter turns into a Fire/Psychic type and Gen VII's fire starter becomes a Fire/Dark type, but the fanbase appears to suffer a collective meltdown when it is revealed that the starter becomes bipedal (and Delphox and Incineroar do). Incineroar can even pass for a Fire/Fighting type since it draws inspiration from a Heel wrestler and learns a lot of Fighting-type moves.