In order to understand pokemon origins first we must understand what a pokemon actually is.
Pokemon are not biological in the way that animals and humans are in our world, they are entities born of thought and emotions that become sentient matter (I would have said flesh but that isn't really what we're dealing with as they wouldn't be able to go into pokeballs then and ghost pokemon would be solid etc). This is similar to the concept of tulpas in Buddhism or thought-form entities, with a few tweaks, and something that Gamefreak are obviously familiar with: Japan's main religion is shinto-buddism and in any case they based a number of starters on charactors from the story and tv series "Monkey" where the main character is created like a tulpa or pokemon.
In fact, talking about Money (which was Japan's most popular show when Tajiri, Sugimori and Masuda were growing up) the origen story of Monkey at the start of every episode is basically the same thing they used for pokemon, although on a more idustial scale (
http://www.youtube.com/watch?v=88y4ttqaW6U ). It would also explain comments made in XY about eggs not being actual eggs but more 'cradles'. The 'egg' must accompany a trainer on their adventure (or just biking around a tower more likely) in order for the trainers thoughts and will to give it form then it can 'hatch'.
But why are there pokemon in the wild where there aren't humans to hatch them and what about pokemon created by Arceus himself? well that is simple to explain. You see... people are pokemon. Perhaps not quite the same thing as pokemon, but similar enough to potentially become pokemon after death as seen most explicitly in the case of Yamask.
