The world of Pokémon is a mysterious place, with gameplay mechanics, the animé, and even the pokédex entries becoming the source of weird mysteries. The most fanatic constantly attempt to solve such mysteries, and that resulted in countless theories and straight-up creepypastas. Here are a few questions that captured my imagination, and the best explanations I could come up with.
The Mystery: Perhaps the favorite mystery Pokémon fans attempt to solve is "Who is Cubone's mother?", while ironically, this is also the most pointless one. The two most popular theories are Kangaskhan and Charizard (despite the obvious evidences to the contrary, like different skin color, different typing, the lack of fire at the end of the tail, and the fact that Cubone can be male, while Kangaskhan cannot). Besides, I thought it's been obvious from Day 1 who Cubone's mother is. (It's Marowak. You're welcome.)
Anyone who ever breeded a Cubone since Generation II knows that it already hatches from the egg with the skull mask and weapon, meaning both of those things are a part of his anatomy. Further evidence is Pokémon Origins, which shows a very much alive Marowak protecting her baby Cubone, who already wears the skull mask. Obviously, the "Skull of the dead mother" story is a lie, a fake rumor in the Pokémon world. The real mystery is... where does the rumor come from?
The Theory: I am forced to assume that male Marowaks are the pickup artists of the Pokémon world. Again, weird stuff, bear with me. Pickup artists are men with low self-esteem who make up for their insecurities by objectifying women and attempting to have sexual intercourse with as many of them as possible. And Marowaks have plenty of things to feel insecure about. They are a little bit on the short side, and they're not exactly muscular either. Also, it seems they think their face is ugly (they are born with masks on, for crying out loud!). They do their best to compensate for these by acting tough. Marowaks are known to be very aggressive, and with the Thick Club, their Attack stat is huge, making them heavy hitters. Hitting things doesn't get the bed warm, however, and because of the low self-esteem, Marowak is desperate to... bone. So he came up with a sob-story.
Losing a parent at such a young age has horrible childhood written all over it, which makes this tough guy an emotionally vulnerable tough guy (the kind of tough guy that gets the girl). Also, it's an important detail that the story is never about the skull of the dead father. It's always about the dead mother, the female parent. This makes female Pokémon of compatible Egg Groups think "Poor guy. He lost an important woman in his life. He needs another important woman in his life. Maybe... I could be that woman". And BAM! The trap is sprung. Yet another naïve girl. GO TEAM BONE!
The Mystery: In previous games, Shinies were few and far between. With a measly 1/8192 chance of a Pokémon being Shiny, many players went through entire games without finding one (save for the Red Gyarados in the Johto games). In the Generation VI games, not only the chance was doubled, to 1/4096, but several relatively simple methods were introduced to increase those chances even further. While still relatively rare, Shinies are more common than ever before, with most players having at least a box full of Shinies. So what happened?
The Theory: Incidentally, Generation VI also introduced the entirely new concept of Mega Evolution, which is possible because of Infinity Energy. In the ORAS Delta Episode, Zinnia says that there is another parallel dimension that doesn't have Infinity Energy or Mega Evolution (basically, the dimension Generations I-V take place in). Now, Shinies also exist in that dimension, but they are much, much rarer. So it seems there is a connection between Infinity Energy and the chances of a Pokémon being born as Shiny. Shininess is a rare genetic trait that is decided by birth, after all. It would also explain why a Shiny sparkles upon appearing, because Mega Evolution itself comes with a similar, although much more visible effect.
The Mystery: In the new timeline where Mega Evolution is possible (started by X/Y), a number of Pokémon can transform into temporary powered-up forms with the aid of held items called Mega Stones. These were not created by humans. So how come an artificial Pokémon like Mewtwo has not one, but two Mega forms? If anyone should have a Mega Evolution, it's Mew, because he is the original one, while Mewtwo is only a modified clone. (Also, it would have been a cool easter egg if Mewtwo's Mega Stones also worked on Mew.)
The Theory: In this new timeline, Mewtwo was created by paranoid scientists to protect mankind from the two most powerful known Pokémon in existence, Mega Rayquaza and Arceus, should either of them ever turn against humanity. So they took Mew's DNA and used it to make the ultimate Pokémon. The result was indeed very strong, but still not strong enough to counter those powerhouses. So the scientists started researching Mega Stones and Infinity Energy, until they finally managed to artificially produce two special Mega Stones to aid Mewtwo in such a hypothetical battle.
Mewtwonite Y greatly boosts Mewtwo's Special Attack, and increases its base stat total to 780. Mega Rayquaza's base stat total is... also 780. Coincidence? This, along with Mewtwo being capable of learning powerful Ice-type attacks such as Ice Beam and Blizzard, would make the Genetic Pokémon humanity's best bet against Mega Rayquaza, should the legendary dragon ever go on a rampage (even with Delta Stream lowering the damage of those moves). Mewtwonite X, on the other hand, not only greatly increases Mewtwo's Attack, but also adds a Fighting sub-type. While Arceus can change his type with its plates, its original type is Normal. Thus, Mega Mewtwo X would not only have a higher base stat total than God, it would also have a type advantage to it.