50) [1st GEN] Analysis of Generation I, Part 5/5: Red, the Champion Despot

After conquering the Elite Four, Red became its leader. However, lacking understanding of things like human emotion, he was horribly unfit for the role of leader. Red became known as a despot, inspiring the hatred of all of Kanto. Under his leadership, the skills of the Elite Four atrophied. Red was blind to the rumblings of rebellion throughout Kanto, but was not blind to the fact that his skills as a trainer were growing dull. To rectify this, he planned a hiatus during which he could train alone on Mount Silver.
At the time that the Elite Four's skills were atrophying, the Kanto gym leaders continued to gain strength. Eventually, Red was the only member of the Elite Four who was stronger than any of the Kanto gym leaders, and when Red left for Mount Silver, the Kanto Gym leaders staged a rebellion. Lorelei and Agatha were either killed or fled into hiding. Bruno, being among the more benevolent rulers of the Elite Four, was allowed to stay. The Kanto gym leaders were not able to defeat Lance's powerful dragons, but after seeing Agatha and Lorelei disappear/get killed, Lance admitted that he had no desire to see the current system continue. The Kanto gym leaders allowed Lance to stay as league champion, and stationed one of their own, Koga, on the new Elite Four. (Koga's daughter, Jasmine, replaced him in the Fuchsia City gym.) Red, meanwhile, continued his training atop Mount Silver. He remained in total isolation until three years later, when he received his first human visitor: a young boy named Gold.

49) [1st GEN] Analysis of Generation I, Part 4/5: Emperors of Kanto

The Kanto region is controlled by four elite emperors, otherwise known as the Elite Four. Kanto is governed under what is essentially a feudal system, with local rulers residing in "Gyms," surrounded by loyal followers/apprentices. The Elite Four is aware of the possibility of a trainer raising Pokemon even more powerful than their own. To prevent such an individual from attempting to stage a violent revolution, the Elite Four has extended a generous offer: anyone who is able to beat them is allowed to join their ranks. Many trainers dream of becoming rulers of the world, but few possess the skill needed to make it even past the first few gyms.

48) [1st GEN] Analysis of Generation I, Part 3/5: Experience Gain

When Pokemon participate in battle, an adrenaline-like response kicks in, allowing the use of combat abilities like summoning lightning or breathing fire. As this happens, Pokemon exude large amounts of radiation. Their adrenal response also leaves them susceptible to radiation exuded by opposing Pokemon during combat. This radiation causes Pokemon to mutate, and the extent of these mutations is proportional to the strength of the opponent. Face a terrifyingly-strong opponent, and high radiation levels and increased susceptibility will lead to rampant mutations. Weaker foes, conversely, will have little impact on a Pokemon's physique.
These mutations cumulatively add to a Pokemon's strength, and sometimes manifest themselves in the form of increased abilities or appendages. For example, Bulbasaur might sprout some vines, allowing it to use the move Vine Whip. Other times, the mutation is more drastic, causing a Pokemon to mutate into an entirely new form. (Also known as evolution)
Although "leveling up" is the usual way for Pokemon to evolve or learn new skills, there are also artificial stimulants that can be used to enhance a Pokemon's combat abilities. You can call them "performance enhancing drugs" if you like, but "Technical Machine" also works. Evolution stones are just high concentrations of chemicals that cause certain Pokemon to mutate.

47) [1st GEN] Analysis of Generation I, Part 2/5: Pokeball Mechanics

A Pokeball leaks radiation proportional to the mass of the Pokemon contained within, and the amount of radiation that the human trainer can safely withstand is proportional to their own body mass. This is why many young trainers like Youngsters and Lasses have lightweight Pokemon like Rattata and Jigglypuff, while heavy Pokemon like Geodude and Onix are always carried by a large and muscular Hikers. Of course, the radiation of those balls adds up, so most people are only capable of carrying three or four Pokeballs at a time, if that many. Gym leaders, being in a static location, don't have to carry their Pokemon on their person, and not being in constant close proximity to their Pokeballs, they can usually get away with using up to five. Red and Blue, being genetically engineered superhumans, have the strength to carry up to six Pokeballs at a time.

46) [1st GEN] Analysis of Generation I, Part 1/5: Origin of Red and Blue

After his work on the Mewtwo project, Professor Oak made multiple attempts at bioengineering a human clone. The first successful attempt used a 650 nanometer laser, which produced a subject that, while biologically human, lacked human emotion. Professor Oak made a second attempt using a 475 nanometer laser. This produced a more refined, more "human" subject who could easily be mistaken for a perfectly ordinary and rambunctious young boy. The first subject was implanted in a surrogate mother living in the town of Pallet, while the second subject matured entirely in Oak's laboratory. The subjects were named "Red" and "Blue" after the colors of the lasers used in their creation. Postpartum, the surrogate requested to raise subject Red. Professor Oak obliged, and chose to raise subject "Blue" as his own grandson.

45) [HISTORY] Mass Extinction

 Credit goes to ninja1121 for submitting this theory.

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.

35) [EVOLUTION] Messed up evolution #4

34) [ANIME] Ash's Age #2

At least one day passes in a Pokemon episode, normally at the end of the episode as well, which means that each episode is one day. In some episodes, two or more days can pass but only a few that it won't effect results drastically. ~760 episodes of Pokemon have aired so far, meaning that almost 2 and a half years have passed since Ash began his journey, so I submit to you that Ash has only slightly changed. Comparing him from is present to past counter part this can be seen by hair length and other slight changes.

This would put Ash anywhere from 12 to 14 years old as of 2012.

33) [5th GEN] Religiously Inspired Pokemon #3

According the to Bulbapedia, during the course of its evolution Snivy gradually lost its legs. At the start of Paradise Lost, Lucifer/Satan looks like the rest of his fellow angels, with the notable exception that he is "fallen" since he has gone against God. When he returns to Hell from Earth after tempting Eve, and thus Adam, in the guise of a serpent, he and the other demons receive their punishment: turning into snakes.

Serperior's Dream World Ability is Contrary. According to Bulbapedia, the ability's Japanese name is "Devil's Advocate."

Serperior's name is supposedly a combination of "Serpent" and "Superior" (Or "Warrior," which, although a bit of a stretch, might make sense). This makes sense since Satan is not only associated with the Serpent, but also as the ruler, and thus most "superior" being, of Hell.

Serperior is a Grass type, although there isn't any indication in the name. Perhaps this was because of the Serpent's association with the Tree of Knowledge?

32) [MECHANICS] Fresh Water's Potency

Let's assume that the Pokemon War did happen and that it was a nuclear war. Several consequences come with nuclear wars including fallout from the areas bombs were dropped on. What if all of the water in the Pokemon World was irradiated? This would explain why fresh water is so expensive, much more effective at healing than a potion, and why Pokemon can't sip from a water source instead of using a potion or going to the Pokemon Center to get healed.

31) [MECHANICS] The Effectiveness of Bubblebeam

It’s not the water of the bubbles that hurt enemy Pokémon; it’s the moist air inside them.

Before firing, the Pokémon inhales. The air it gathers mixes with the water in its body and super compressed into bubbles.

But these bubbles can only hold for their orb-ness for about a second before popping. So the Pokémon spits them out as fast as it can, ergo like a beam.

When the bubbles pop, they actually explode and spread blasts of concentrated moist air at the target.
So bubblebeam is like a cloud of tiny grenades.

Pokemon saliva may act as an extra layer of thickness, which allows for higher air pressure.