Don't look at me like I'm mad (I am but that's not the point), this is a really cool theory, bear with me!
I was thinking today, regeneration in Doctor Who and evolution in Pokemon are almost exactly the same process. They both involving a glowing light, that spreads over and through the body of the organism and moulds it into the new form, they both occur normally after physical strain from a battle or injury, and they both involve a slight change of physical form and personality, but memories stay intact. So perhaps, just maybe, pokemon are related to time lords. So, here's the crazy bit: What if pokemon where the creatures of Gallifrey, and a time lord, during the time war, used a portal in the multiverse to move them to the pokemon world, in order to save them from the upcoming death of their planet. In other words, what if pokemon are not native to the pokemon world, but originally evolved on Gallifrey?