-Pokémon RBY: Blue's Raticate
The theory is that Raticate was severely wounded in the battle on the S.S. Anne, but was not taken to a Pokémon Center in time, resulting in its death. The reason your rival is in the Pokémon Tower in the first place is to bury and mourn his lost Raticate.
WRONG: Causing all of one's Pokémon to faint wounds them in the same way, so wouldn't all of his Pokémon have died along with Raticate?
FIXED: Raticate was not killed from battle wounds. When Blue's Pokémon were healed at the Pokémon Center, it was discovered that Raticate had rabies. Raticate was put down and buried in the Pokémon Tower.
-Pokémon GSC: Legendary Beasts Are Dead Eeveelutions
This theory goes that a Flareon, Jolteon, and Vaporeon died in the Brass Tower fire and were resurrected by Ho-Oh.
WRONG: The Pokémon could have easily escaped the tower. Vaporeon could put out the fire and Flareon could walk through it.
FIXED: Three Eevee died in the Brass Tower fire and were resurrected by Ho-Oh as Entei, Raikou, and Suicune. Once the tower was rebuilt, a ceremony was held where people attempted to offer Eevee as sacrifices to Ho-Oh, which instead became the first known Flareon, Jolteon, and Vaporeon.
-The First Pokémon
Mew is the "common ancestor of all Pokémon", but Arceus is the "Pokémon version of God."
WRONG: Mew can learn every move in existence, but Arceus can't. Why would the first Pokémon to exist give the later one that much power?
FIXED: Mew was the first Pokémon to exist. Early people began to worship Mew, which it didn't appreciate. Perhaps this resulted in the Great War from X and Y, or the Darkest Day in Sword and Shield. To resolve the conflict, Mew created Arceus, Dialga, Palkia, and Giratina to be worshipped in its stead.
-Cubone: Unlit Charmander Theory
*pictured above
WRONG: From the time it is born, a flame burns at the tip of its tail. Its life would end if the flame were to go out. (Pokémon FireRed Version)
Even the newborns have flaming tails. Unfamiliar with fire, babies are said to accidentally burn themselves. (Pokémon Stadium)FIXED: Charmander's Pokedex entries listed above imply that the tail-flame is lit in-utero, so to fix this theory, we simply have to create a scenario that would prevent this from happening. Perhaps the Charmander fetus sometimes gets too close to the walls of the egg, and as a defense mechanism, it grows spines like those seen on Cubone to push itself back into the center. However, this stunts growth in the tail, meaning it cannot ignite, and the affected Charmander is stillborn. The mother Charizard tries everything to ignite the flame on the baby's tail, but when it proves impossible, she becomes depressed and withers away. However, the baby Charmander is resurrected as Cubone to ease the spirit of its departed mother.
For whatever reason, this does not occur in domestically-bred Charmander, and domestically-bred Cubone acquire their skull helmets genetically.
-Pokemon XY: Lumiose City Ghost Girl
"No, you're not the one."
"I'm going to get help. Wait in the usual place."
These two sentences have puzzled us all since our first adventures in Kalos. Come to think of it, completely random thought, but... why the heck is Mewtwo catchable in these games?
Hm... What if the Ghost Girl is Amber?
Mewtwo is encountered in a cave in both instances, so maybe a cave is "the usual place," like a safe spot or where he can communicate with Amber's spirit. By this logic, "the one" would have to be a Trainer strong enough to catch Mewtwo and try to fill the void in its heart that Amber's death left behind. Amber would go out and search for this Trainer, or "get help." Mewtwo is only catchable in the post-game, once you're the Champion, so it's not out of the question that Amber was looking for Diantha, and only says the player is "not the one" because they're not strong enough yet.