Fun thread! Particularly enjoyed the Hitmonchan sprite, Ditto and meta-anime theories. That last one is immense - how spectacular would it be if, after the last episode, the writers were just like, 'Hah, you thought we'd produce hundreds of episodes of drivel like that non-ironically? You got taken for a ride, son.'
While I've been playing through the main series, I've developed a bit of a theory (I'm sure there are others like it already out there) that links the plot-lines of the main series games, and explains how the protagonist in each one is actually the same character, on one continuous journey. It borrows a little bit from the manga, in terms of the Kanto/Johto Elite Four and most Gym Leaders being evil and high-level members of Team Rocket. It would take a while to flesh out properly, but basically, at the end of each region, some tragedy befalls the protagonist (death of his father, all his Pokemon stolen, etc.), forcing him to relocate and take on another identity elsewhere. After Kanto, Hoenn, and Sinnoh, the protagonist goes to Johto, where people are still talking about his monumental defeat of Team Rocket three years previously. His journey through Johto (and then Kanto again) is a Kill Bill-esque saga wherein he attempts to find and destroy those who ruined his life.
While I've been playing through the main series, I've developed a bit of a theory (I'm sure there are others like it already out there) that links the plot-lines of the main series games, and explains how the protagonist in each one is actually the same character, on one continuous journey. It borrows a little bit from the manga, in terms of the Kanto/Johto Elite Four and most Gym Leaders being evil and high-level members of Team Rocket. It would take a while to flesh out properly, but basically, at the end of each region, some tragedy befalls the protagonist (death of his father, all his Pokemon stolen, etc.), forcing him to relocate and take on another identity elsewhere. After Kanto, Hoenn, and Sinnoh, the protagonist goes to Johto, where people are still talking about his monumental defeat of Team Rocket three years previously. His journey through Johto (and then Kanto again) is a Kill Bill-esque saga wherein he attempts to find and destroy those who ruined his life.