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The infamous "you killed your rival's Raticate" theory from the first games. Never played seriously nowadays outside of creepypasta.
The names of Silver, Kris, Leaf, Barry, and Hugh may fall under this. The first three are named after their games, Barry is named after his anime counterpart, and Hugh is the character's default name.
Trainers all beginning their journeys at the age of ten. While this is canon to the anime, the games have made no such statement.
A "subtrope" of this is the main protagonists of each game being ten. The only protagonists to have a canon age are Red and Leaf, who are eleven. Hilbert and Hilda are implied to be much older.
and Pokémon Colosseum being canon to the handheld games.
Pokémon XD: Gale of Darkness The Kanto and Hoenn games taking place simultaneously.
The three Pokemon that died in the Burned Tower and were revived as Entei, Raikou, and Suicune are believed to have been a Flareon, Jolteon and Vaporeon respectively. This is backed up by the three having the Eeveeloutions normal abilites as their Dream World Abilities.
Professor Oak being the rival's paternal grandfather, and as such the rival's last name being Oak. Canonized in FireRed/LeafGreen.
The Pokemon that Bill was fused with being a Clefairy. Canonized in FireRed/LeafGreen.
Game!Silver being Giovanni's son. Canonized in HeartGold/SoulSilver.
Giovanni committing suicide at Tohjo Falls. Jossed in Black 2/White 2.
The ever-so-popular fics detailing original characters receiving a starter, defeating 8 gyms, fighting a villain team, and becoming the Champion. Common details include:
The normal starters being unavailable, resulting in the protagonist getting a starter outside the normal trio.
In the early days of the fandom, this was always an Eevee. ALWAYS.
The villain team is always Team Rocket, Cipher, or Team Plasma. (Magma, Aqua, and Galactic? Who are they?)
The Pokemon League being anime-styled, in which there is a tournament every year or so determining who gets to fight the Elite Four.
After Action Report fics based off the writer's actual run of the game. Quality tends to vary a lot in these ones. If they ever get finished.
In anime-based fics, an established character turning out to be Ash's father.