44) [6th GEN] Sound and Light Types

 This theory is merely speculation and will be either confirmed or busted upon the release of Pokemon X and Y.

43) [1st GEN] Origins of Mewtwo #1

Katsuhiro Otomo's Akira was written in the mid-80s with an animated film adaptation in 1988. Pocket Monsters, as an idea, sprung up at least in 1990. In Akira, scientists try to replicate the insanely powerful, but child-like psychic named Akira by experimenting on an angsty, older boy named Tetsuo. When Tetsuo's psychic powers go out of the scientists' control, he desires to confront Akira, to see who is more powerful. In Pokemon, the psychic-type Mewtwo was created by scientists to replicate the psychic-type, child-like Mew and also went out of control. In the anime film, Mewtwo also wishes to face Mew in battle, and also has his share of angst.

42) [DITTO/MEW] Ditto is NOT a Failed Mew

So how does the Mew/Ditto work any way other than going off of the stats (strengths in categories) and the color? Other Pokemon could have the same stats as Mew, but you would never call them to be failed attempts of Mew. This, combined with the fact that Cinnabar is the only lab that had such a major accident that the lab had to be abandoned. This would result as it to be the only area where failed/in-progress experiments could be outside the testing area.
Thus, the radiation/psychic energy given off by the lab after it was abandoned stimulated the stem cell clusters to life, without the cells first forming, and giving them the ability to copy other Pokemon (just like organs in real life), yet also return to their amorphous state.

41) [1st GEN] Nuzlocker Blue

Blue/Gary was actually a Nuzlocker. He made a special rule after the first battle he had that his battles against you didn't count. He lost his Raticate, yes, but in an unrelated battle after the SS Anne. He's not a bad trainer; he's an extremely good Nuzlocker who has only ever lost to one person: you.

40) [EVOLUTION] Cyborg Kabutops

39) [2nd GEN] The Tin Tower Reincarnations

38) [EVOLUTION] Is Deoxys a... canonized Missingno?

Missingno is a glitch, which are tangentially related to computer viruses, while Deoxys was a biological virus that had been mutated by a satellite. Likewise, both Missingno and the Normal form of Deoxys have massive offensive stats but nearly non-existent defensive stats. Missingno also appeared in Generation I, and while Deoxys did exist in the Ruby/Sapphire data, it was not until the remakes of Generation I that there was an event to capture him.

37) [EVOLUTION] Cubone is not a baby Kangaskhan

Here's a different take on the baby Kangaskhan theory.

In the real world, boomerangs were used to hunt kangaroos.

Theory: Marowak have various tribes all over the world, and when these tribes were beginning to be formed, to tell the difference between members of the tribe, the original members all went on a mass hunt of Kangaskahn, took their skulls, gave them tribe markings, and used them as headdresses.

When each member pass away, their eldest child took their headdress and wore it, part in remembrance, and part to honour tradition. This practice still continues to the present day.

We interpreted the Pokedex entry wrong, they don't wear the skull of their ancestor, they wear the skull their ancestor wore as a headdress.

36) [MECHANICS] Just like us

All of Psychic's weaknesses are common fears. Fear of ghosts, fear of the dark and fear of bugs are all common fears, and since psychic has to do with the mind, it would make sense why they're good against it.