The Pokémon anime is the most famous adaptation of the games and the second most marketed media after the original (with the famous movies made to promote the new mons that everyone know about). It's also known to be highly different from the games, but PokéSpe is different, the manga is recognized as the most loyal adaptation of the games and this section is to highlight that: the differences between the manga to the anime compared to the games.

Note: This a non-exhaustive list of general differences between the manga and the anime, I am gonna let the differences between the characters to different sections.

• The main characters change with each arc, the protagonists are the same playable characters (and rivals until 4th gen) as their game versions.
• There is a timeline and the characters grow up with time, per example all the dex holders of the 1st arc (Red, Green & Blue) are already in their early 20s by the X & Y arcs.
• Pokémon trainers can catch legendary and mythical pokémon (and the ultra beasts), that are treated like normal pokémon instead of gods or something.
• Pokémon trainers give nicknames to their pokémon, and mostly of the protagonists do.
• Most of the legendary pokémon don't have a huge impact of the story by themselves, they're sometimes used by the villains of the manga, but they aren't the sole focus of the story (I am talking about the movies here), not even Mewtwo.
• Porygon isn't polemic in the manga (I think every anime watcher what I am talking about lol), so he appears in the manga and is owned by Green (later he even evolve).
• The gym trainers, elite 4 members and pokémon champions have more depth and personality and some even are villains in the story.
• Most of the towns, locations, routes and secondary characters are based on their game versions.
• Not all the dex holders has the goal of becoming pokémon champion or challenging the pokémon gyms. And each arc has a different storyline around these goals.
• While all dex holders owns a starter (except Whi-two), not all the pokémon were give to them by the professors, some were stolen from the professor, some were supposed to be given to other person and some starters were gotten from other people.
• Most of the dex holders pokémon evolve to their final forms (there are some exceptions like Diamond's Munchlax).
• Team Rocket only exists where they appeared in the games (1st gen and the remakes), there is no Jessi and James with a talking Meowth in the manga and they're actually villains here.
• The manga has a more dark tone than the anime, notably examples are the zombie Psyduck and the Arbok that was cut in half. Some villains are actual bad guys, in the X & Y arc, per example, they actually destroyed one city and the protagonists are running for their lives. Also, some characters do actually die.
• The Pikachus stay chubby in all the manga arcs!
• The villains use their pokémon as weapons instead of just battling with them, per example electric type pokémon are used to give shock to their trainers and ice type pokémon to freeze them or the environment.
• Each protagonist (Pokédex holder) has a distinct unique skill that differs them from the other pokémon trainers.
• Misty and Brock stay as gym leaders in their respective cities and never follow Red around (Ash's counterpart, since they're both based on the protagonist of the games). They go out of their way to defend their cities from the Team Rocket though.
• The art style is better in the manga!
• The colored part of poké balls are transparent and pokémon can be seen from outside in a miniature version.
• Pokémon make sounds instead of repeat their own names.
• There are HMs in the manga.