(Now this is obviously overthinking it but, isn't that what this site is for?)
There are a lot of different pieces of evidence that point to one possible theory that Pokemon in the Pokemon universe don't actually exist. I propose they are simulated creations or some kind of digital creation (possibly procedural) generated to occupy youth. Perhaps it's been so long since they were created that the people have forgotten where they even came from (cf scientist in series who thought they came from space — although maybe that's true but they were designed by beings other than humans).
Compare to modern days where video gamers are often celebrities and compete in high level tournaments. Take this to an extreme where the real world is infused with the gaming world until the line between the two becomes quite fuzzy.
I think this theory explains why Pokemon are so obedient — because they were designed to be.
Evidence:
* Pokemon almost always look identical, except for mostly minor differences between males and females (and randomly certain varieties have larger differences between the sexes, e.g. Nidoran and Nidorina)
* Pokemon fit inside Pokeballs and clearly turn into some form of light or energy when entering them. Plus they can be transmitted electronically and yet there is no apparent way for humans to travel via teleportation.
* Pokemon seem to be mostly sentient, capable of understanding English despite usually not being able to speak it (with the exception of Team Rocket's Meowth, which just adds credence to this theory)
* Pokemon don't usually seem to die, although characters in the series often seem pretty worried about their Pokemon's health. 802
Charmander and its evolutions seem to be an exception since if its tail flame is extinguished, it dies (although I'm not sure if this has ever been actually shown to occur). (Edit: relevant answer on Anime SE)
* Pokemon usually instantly go from wild to tame without much training as long as the trainer asserts themselves properly or demonstrates their friendship.
* Pokemon evolve instantly into new, often extremely different (e.g. Graveler to Golem) forms.
* Pokemon appear to be distinct from normal animals, as certain animals are mentioned in the series (more here)
* Pokemon trainers are often shown to be quite young, even in gyms and the higher level tournaments. Older individuals are often academics interested in studying Pokemon.
* The ancient Pokemon discovered underground in the original series by <PERSON> supposedly had been there for a long time
* Pokemon can be evolved using seemingly magical stones
* Any kind of Pokemon can hatch from an egg, despite the fact that there are a variety of different gestation methods in animals
* Pokemon can be very powerful, far beyond what would be physically possible
* Pokemon can seriously injure each other, but generally while they can attack humans, they don't seem to permanently damage them (e.g. Charizard shoots flames at <PERSON> all the time but he never seems to be harmed, at least not according to what fire like that ought to do to a person)
* Pokemon hatch / evolve into forms with accessories that wouldn't form naturally (Machoke/Machamp's belt, Hitmonchan's gloves, Cubone's skull/bone, Polywhirl/wrath's gloves), Primeape's cuffs etc
* Trainers have to actually encounter a wild Pokemon to fill in its field in their Pokedex, even though they have already been encountered before. Plus the Pokedex is able to identify Pokemon very easily.
* Plus a lot of the points from this other answer apply
Edit: one potential problem with this are the Pokedex entries that are shown about Farfetch'd, which say it makes a delicious meal and has been hunted to near extinction. 671