List of differences between the games and anime

This is a list of differences between the main games and the main anime series that the anime is based on the games, but they included a lot of differences from the source material for the main anime series such as Team Rocket appeared more than the Kanto and Johto saga, Red was replaced by Ash, Orange Islands are added in the anime, and Ash's anime exclusive rivals, etc. (but, this list isn't included from Pokémon Origins nor Pokémon Generations).
==List of differences from the main series games==
This is a list of changes happened in the anime that were got some differences from the main games.
*Ash, Gary Oak, and Delia Ketchum replace Red, Blue, and Red's mother in the anime series.
*A lot of game characters such as Green, Janine, Wally, Hilbert, Hilda, Hugh, Nate, Rosa, Calem, Elio and Selene never appeared in the anime.
*Ash takes the other male protagonist's role in the other seasons.
*Ash gets a Pikachu instead of one of the Kanto starters as his first Pokémon.
*Spearow is shown to see in black and white in the first episode, but this was never explained in the games.
*Ho-Oh was first seen in the first episode, but Ho-Oh wasn't supposed to appear until in the Generation II games.
* Brock appears as a former Gym Leader in the anime, but in the games, he is still a Gym Leader.
* Brock has shown to get interest in loving with girls in the anime. This trait was never shown in the mainline games.
*Misty wasn't the Gym Leader from the start of the anime then, she later became the Gym Leader after the Johto series, but in the games, she is still a Gym Leader.
*Misty has three sisters, Daisy, Violet, and Lily were added in the anime.
*Brock has his entire family (Flint, Lola, and his entire siblings) added in the anime.
*Ash has companions in the anime, whereas the playable characters goes alone in the games.
*Ash doesn't lose money nor black out after losing a Pokémon Battle.
*Pokémon evolve during in the battle, but they only evolve (except for Mega Evolution) after winning battles in the games.
*Ash doesn't receive any Master Balls in the anime, even though they're awarded after certain events in the games.
*Misty, Brock, Cilan, Iris, Clemont, Bonnie, Lana, Lillie, Mallow, Sophocles, and Kiawe are main characters in the anime, as opposed to minor characters like they were in the games.
*Team Rocket have a lot of anime exclusive members added in the anime such as Butch, Cassidy, etc.
*Gyms in the anime have a limit as to how many Pokémon the challenger can use against the Gym Leader, but in the games, the player can use all Pokémon they have in their party.
*Bill has Green hair instead of brown.
*Team Rocket never disbanded in the anime.
*Guns were added in the earlier parts of the anime while there is no sign of guns ever shown up in any of the mainline games.
*TM and HMs were excluded in the anime.
*Mr. Fuji is a doctor and a head scientist of Team Rocket instead of a kind-heart old man that runs the Pokémon Orphan in the anime.
*Dr. Fuji has hair and a beard instead of being bald and have no facial hair in the anime.
*Dr. Fuji gets killed by Mewtwo instead of kept alive in the anime.
*Dr. Fuji has a family of a daughter that died from a car accident and a wife that were added instead of being single in the anime.
*Dr. Fuji never meet Ash in the anime.
*Giovanni didn't battle Ash at the Viridian City Gym like he does against the player in the games.
*Giovanni obtained a Mewtwo in the original series, but he doesn't have one in the games.
*Gary was never the Kanto Champion in the original series.
*Agatha and Lance weren't seen in the original series, but they do make an appearance in later seasons of the anime.
*The Orange Islands, Decolore Islands, and their arcs are added in the anime.
*Tracey and Max were added in the anime. (Technically Tracey appears in Pokémon Puzzle League, but it's based on anime instead of the main games)
*Lorelei was renamed as Prima in the 4Kids Dub of the anime.
*Lorelei was from the Orange Islands, but the Orange Islands never existed in the games.
*Lance catches the Red Gyarados instead of Ash or his friends, but in the games, the Red Gyarados is catchable for the players.
*There are no time skips in the anime, and all regions exist in the same universe; each installment of the games are set at different times from each other, and it's implied that the games (starting with Generation VI onward) take place in an alternate universe.
* Misty's appearance in the anime remains the same from the Generation I games, whereas her style changes after the Generation II games.
*Giovanni appeared in the Generation II Johto anime series, but he didn't appear in the Generation II games.
* Gary doesn't take the role as Viridian City Gym Leader after Giovanni's defeat, instead becoming a Pokémon Researcher, and Agatha takes the role as the Viridian City Gym Leader; in the games, Blue becomes the Viridian City Gym Leader after Giovanni's defeat.
*Jessie, James, and Meowth were seen again in the other series; they only appeared in Pokémon Yellow version and Pokémon: Let's Go, Pikachu! and Pokémon: Let's Go, Eevee!.
*The Battle Frontier from Pokémon Emerald version were in Kanto instead of Hoenn.
*Gold/Ethan's and Kris's name from the Generation II games were renamed as Jimmy and Marina in the anime.
*Contests have battles added in the anime, but they don't have battles in the games.
*Shelly and Tabitha were renamed as Isabelle and Harlan in the 4Kids Dub of the anime.
*Juan takes Wallace's role as the Gym leader like from the Pokémon Emerald version.
*Wallace hosts the Wallace Cup and he was a former Gym Leader and Champion in the anime.
*Ash didn't go to the Sevii Islands, but Sevii Islands only appeared in one episode in Pokémon Chronicles as a minor location in the anime.
*Paul takes Barry's role at the start of the Pokémon Diamond and Pearl anime; Barry himself appears in the later seasons of the Sinnoh anime series.
*Barry also has an Empoleon instead of an Infernape because Ash chose Turtwig and Dawn chose Piplup.
*Pokémon Hunter J and her crew were added in the anime.
*Lyra appeared in a few Sinnoh episodes, but she only appears in Pokémon HeartGold & SoulSilver Version which is in Johto.
* The Johto Festival in Sinnoh was an anime-exclusive event.
*The Lake Trio were successfully captured by Hunter J instead of Saturn, Mars, and Jupiter, like they were in the game.
*Professor Fennel's assistant and younger sister, School Kid Amanita didn't appear in the anime.
*Lenora's Herdier was already a Herdier in the game, but in the anime, it's shown first a Lillipup and then a Herdier.
*Ash didn't get the Legend Badge and have a Gym Battle against Drayden like from Black and White series, instead battling Roxie from Virbank City Gym and obtaining the Toxic Badge instead as his eighth Unova Gym Badge.
*Trip, Stephan, Cameron, and Virgil have a major role in the anime instead having a one-shot minor role like from the Black 2 and White 2 Japan-only event.
*Cheren was replaced by Trip as the rival and has a one-shot minor role as a Gym Leader with his attire from Black 2 and White 2.
*Charles appears to be different in the anime, and his Mighty Excelgor is added in the anime and also, he never explains Triple Battles.
*Elesa has 1 Emolga instead of 2 and Elesa has a Tynamo replaces the second Emolga.
*Skyla has a grandfather in the anime.
*Skyla was introduced in the anime as rushing the gym battle with laziest way to use type advantages comparing to opponent's types due to she wanted flying planes more than do Gym Battling, in the games, she acts responsible for a Gym Leader.
*Cilan did showed some competitive Pokémon Battling skills in the anime while the games that he was shown to be weaker when Pokémon Black Version 2 and Pokémon White Version 2 happened.
*Chili and Cress didn't resign their Gym Leaders positions in the anime since Pokémon Black Version 2 and Pokémon White Version 2 showed Cilan and his brothers had been resigned their Gym Leader positions to show how weak they became after Pokémon Black Version and Pokémon White Version.
*Caitlin appears in her Unova Elite Four attire, but not in her Sinnoh Frontier Brain attire. This is because the time skip that happens in the games never happened in the anime, and Ash never battled the Sinnoh Battle Frontier.
* Castle Valet Darach doesn't appear in anime nor he was mentioned by Caitlin due to Ash never fought the Sinnoh Battle Frontier.
* N isn't an antagonist in the anime series of the Unova series and didn't defeat Alder, but he appears in the later seasons of the Unova series and not at the beginning.
*Ghetsis never wore his outfit from Black and White in the anime, he wore his Black 2 and White 2 outfit instead.
*Team Plasma showed up in the later season in the Unova series instead of appearing in the first Unova season.
*Team Plasma Grunts only used their Neo Team Plasma outfits instead of the first outfits from Black and White, however, Team Plasma Grunts were originally going to be planned to have their first outfits in the both canceled episodes in the Pokémon: Black & White anime.
*N doesn't own any Pokémon in the anime nor captured Zekrom nor Reshriam.
*Anthea and Concordia became former members of Team Plasma in the anime, instead of staying at Team Plasma like they do in the game.
* Alder keeps his title as the Unova Champion in the anime, until he is beaten by Virgil, but in the game, he is beaten by N.
*Iris doesn't get the role as a Gym Leader nor the Champion in the original Black & White anime. However, Iris becomes the Champion during at Pokémon Journeys: The Series off screen and explained her battles in the Unova League. 
*The Village of Dragons appeared in the anime, but was only mentioned in the games.
*The Reveal Glass was located at the Ancient Temple in the sea, but it was obtainable in the Abundant Shrine in Black 2 and White 2.
*Alder did not actually own a Volcarona in the anime, but only in the games. In the anime, he owns a Bouffalant instead.
*Roxie chooses 3 Pokémon in the anime, but she only chooses 2 in the games. Also, in the game, she had a Whirlipede, but in the anime, she had a Scolipede instead.
*The Seven Sages did not actually appeared in the anime, but only in the games, besides that Ghetsis is the only of them to appear in both the games and in the anime.
*Alexa appeared near at the end of the Unova saga, but her debut from the games was Pokémon X and Y.
*Ash got a Froakie instead of a Chespin because Serena got a Fenniken and hasn't evolved into a Delphox yet. Also in the anime, the Braixen is as female when in the games, it's a male.
*Serena's appearance in the anime has a few minor cosmetic differences from the games.
*Serena didn't get a notice from Professor Sycamore for her Pokémon nor meet Shauna, Trevor, and Tierno.
*Clemont and Bonnie have a father named Meyer in the anime.
*Clemont has more inventions that only appeared in the anime.
*Miette is only Serena's rival in the anime.
*In the anime, Pokémon Puffs appear outside of Pokémon-Amie.
*Pokémon Puffs Bake-off is added in the anime, but the contest doesn't appear in the games.
*Siebold uses Mega Evolution in the anime with his Blastoise, but he neither uses Mega Evolution nor has a Blastoise in the games.
*Korrina only has one Lucario instead of two.
*Korrina begins her Mega Evolution training in the anime, but in the games, she already knows how to use Mega Evolution.
*Korrina's Lucario loses control while Mega-Evolved, but this never happens in the games.
*Shauna, Trevor, and Tierno get a Bulbasaur, Charmander, and Squirtle in the anime, but Shauna doesn't receive one of the Kalos starters like from the games.
*Gurkinn has a Blaziken and Lucario, and also uses Mega Evolution on Lucario.
*Gurkinn fights Korrina during her training, but he never fights her in the games.
*There were more trainers using the Mega Evolutions in the Kalos series of the anime, but in the games, the players, rivals, Korrina, Diantha, and Lysandre were the only ones fighting using the Mega Evolution in Pokémon X and Y.
*In the Reflection Cave, there was a portal to go to another dimension, but this was never happened in Pokémon X and Y.
*Tierno, Trevor, and Shauna receive their starter Pokémon at Professor Sycamore's lab instead of in Vaniville Town.
*Trevor doesn't obtain a Pikachu like in the games.
*Shauna posts her Trainer Videos in the Pokémon Center, but this only appears in the anime.
*The Shalour City Gym is located at the Tower of Mastery instead of in Shalour City.
*Korrina uses her Lucario and with the Mega Evolution during in the Gym Battle with Ash, but in Pokémon X and Y, she uses her Hawlucha at the Shalour City Gym and she fought with the Mega Evolution at the Tower of Mastery.
*Neither Ash nor Serena receive the Mega Ring at the Tower of Mastery after defeating Korrina like the player does in the games.
*Tierno, Trevor, and Shauna don't appear with Ash, Serena, Clemont, and Bonnie at the Tower of Mastery like they do in the game.
*Steven Stone's Metagross is shiny instead of a normal color from the games.
*Mallow, Kiawe, Lana, and Sophocles aren't trial captains in the anime, unlike Ilima and Acerola.
*Harper and Sarah more look like their big sis instead of using the twin sprites appearance from the games.
*Lillie is a Pokémon trainer and obtains an Alolan Vulpix that she names Snowy. In the games, she was never shown becoming a trainer until after Pokémon Ultra Sun and Ultra Moon.
* Lillie and Gladion are revealed to be Lusamine's children in Episode 8 of the Sun and Moon arc when her Butler, Hobbes, tells Ash about the photo of Lillie and her family when she was a young girl. In the games, both are revealed to be Lusamine's children shortly before she left for Ultra Space.
*In the anime, Lillie had a phobia of Pokémon and was unable to touch them for a time. She had no such character trait in the games.
*In the games, Lillie resides in Professor Kukui's loft with Nebby. In the anime, she lives at her family's mansion with Snowy, and Ash uses the loft instead.
*Lusamine is well-meaning towards Lillie in the anime, if only a little self-centered, completely lacking the animosity she has towards her children for leaving her in the games.
*Gladion was not affiliated with Team Skull.
*Nebby was found by Ash on the way to the Pokémon School in the later episodes instead of taken by Lillie during her escape in the Aether Paradise in the games.
*Ash gets an Electrium Z instead of Fightinium Z after winning Hala's Grand Trial in the anime. Although he was originally going to get Fightinium Z.
*Olivia has the Midday Form of Lycanroc instead of the Midnight Form like in the games.
*Professor Kukui and Professor Burnet were already married in the game's plot, but in the anime, they started as single and Professor Kukui proposed a marriage to Professor Burnet after rescuing Lusamine.
*Lusamine didn't become the antagonist in the anime, but in the game, she was the main villain.
*Lusamine gets kidnapped by UB-01 Symbiont and took her to the Ultra Wormhole instead of unlocking the Ultra Wormhole using Nebby and going to the Ultra Wormhole with Guzma.
*Mohn has never appeared in person but only in photos and flashbacks.
**It is also unknown whether he has suffered from amnesia after being sucked into the Ultra Wormhole.
* Poké Pelago doesn't really exist in the anime.
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