Everything produced by GameFreak, Nintendo, or authorized subsidiaries is canonical because they are official media. Yes, even the anime, contrary to the mantra often repeated here. The mainline and spinoff games, the animated show, the movies, the manga, and many other works all fall under the umbrella of the Pokémon universe. Even when portrayals and information conflict, the differing interpretations are licensed by the series creators and given a stamp of approval. Thus, all these works are canonical, even if that might entail multiple "Pokémon worlds" in which the characters, government, and customs vary depending on the universe. The games all likely occur within the same world, but as far as I am aware, there is no official statement that every piece of media takes place on that same planet.
Everyone is entitled to an opinion on the different interpretations of Pokémon over the years, and there is absolutely no rule that you have to like or dislike certain aspects because your preferences are entirely your own. Feel free to trash what doesn't appeal to you and celebrate the media that does. Go wild! But the assertion that there are pieces of Pokémon media that are more canonical than others, simply because you don't want to consider the parts you despised as part of the same franchise as the parts you loved, is totally false.
