This aims to be a comprehensive list of similarities and differences between the manga and the respective Pokémon games. This is an ongoing section that I'll add more content to while I reread the manga. The plan is to be 100% accurate, and if you find something wrong here, feel free to contact me. It'll be ordered in manga arcs.

Warning: This page is full of unmarked spoilers.

• The buildings are identical to the games.
• The maps are also the same as in-game.
• The Pokédex entries are the same as the in-game entries (it's even pixelated!).
• The Pokémon attacks affect the trainers as they affect the opposing Pokémon (The Team Rocket purposely attacks the trainers to hurt them).
• The Pokémon sometimes attacks the environment around them (think of the Duelist Kingdom Arc of Yugioh).
• Brock's gym looks like a wrestling ring and he gives out flyers to accept new trainers instead of just waiting for them to come.
• Misty is from a wealthy household, she lives in a mansion and has lots of maids.
• Cerulean is a Venice-like city, it has canals and gondoliers.
• Erika is also from a wealthy household, she is the daughter of the richest family in Celadon and she has a bunch of followers.
• Trainers can actually carry more than 6 Pokémon at a time (it shows Red with a bunch of Poké balls in his belt before he met Bill and learned about the Pokémon PC).
• Bill is transformed into an anthropomorphic Rattata when using his Pokémon teleportation machine.
• The S.S. Anne is a cargo ship instead of a cruise.
• Half of the gym leaders are part of Team Rocket.
• There is a forest crawling with bug Pokémon in route 11.
• Other secondary characters that are Pokémon trainers are actually trainer classes from the game.
• Lavender Town is Arabic-inspired.
• Mr. Fuji was never a scientist, he takes care of Pokémon in Lavender Town; he had a Doduo that died and he couldn't bury him in the Pokémon Tower because of the ghosts but he never went there himself.
• There is no Marowak ghost in the Pokémon Tower and the "ghosts" in Lavender Tower is just a cover story to a Team Rocket hideout so there is no Marowak's ghost.
• There is actually Pokémon zombies in Lavender Tower (but they are controlled by Team Rocket).
• The Pokédex shows the same message as in the games when a Pokémon evolves.
• The Pokédex shows the HP bar of a Pokémon.
• The Pokédex shows the moves of a Pokémon.
• The Rocket Game Corner exists in the same way as the games, Green even won a Porygon there.
• The Eevee from Celadon is a experiment of Team Rocket and he can change freely in his evolutions (Vaporeon, Jolteon and Flareon).
• The Safari Zone isn't a place to catch Pokémon, it's a place to tour (in a boat) and see wild Pokémon (similar to real-world safaris) and the Pokémon there are notably more aggressive than normal wild Pokémon.
• The logo of the Safari Zone resembles the Jurassic Park logo.
• Pokémon are dangerous, just like their Pokédex entries imply and it's shown in numerous occasions. Examples: An Arbok can spill acid through their mouth (in the Pokémon Tower, Koga's Arbok tried to kill Green's Charmeleon with it), a Nidoking's claws also contain acid and a Victreebel can actually digest people when swallowed (a Nidoking attacked Red and he got his leg hurt and a Victreebel tried to eat him in the Safari Zone).
• There are HMs, they look like wristwatches instead of CDs and Red's Pokémon learned Flash, Strength, Cut and Surf.
• Red searched for HM03 (surf) in the sea bottom while swimming with Poli, on Route 19, instead of the Safari Zone.
• Items in routes/dungeons are inside Poké balls.
• Red got his Pokémon fossil (Aerodactyl) from Giovanni himself.
• In the first chapters of the manga Blaine is a scientist for Team Rocket and he was responsible for creating Mewtwo, later he abandoned Team Rocket and was seen by them as a traitor.
• The Pokémon Mansion is a normal habitable house, probably owned by Blaine, or he used to live there for awhile since Team Rocket looked for him there.
• The Pokémon Lab is Blaine's secret laboratory and is also inside the volcano.
• Saffron is under the government of Team Rocket, the guards don't let anyone go through by land and Sabrina's Mr. Mime created a globe-like barrier covering the city air area.
• The fighting dojo doesn't make an appearance.
• The Pokéedex shows the world map just like in the game (including Red's in game sprite)
• Using all 8 gym badges (except Viridian's gym) Team Rocket fused together Articuno, Zapdos and Moltres into a Pokémon called Thu-Fi-Ze.
• The Team Rocket experiments with Pokémon and they had a plan to use the Viridian Forest as a breeding ground for their experimented Pokémon.
• The Pokémon League is a competition, we know that there is four groups, semi-finals and finals but the requisites to join it are unknown.
• There is a display monitor in the League showing the Pokémon's HP.
• If a Pokémon is thrown out of the ring he is disqualified from the Pokémon League.