>The whole show is a hallucinated attempt by Shinji of Neon Genesis Evangelion to try and preserve his own happiness and sanity.
>Shinji = Ash, Asuka = Misty, Ryoji = Brock, Gendo = Professor Oak, Misato = Delia Ketchum. The Pokemon in general are ways to avoid both fighting and death (Pokemon only "faint", and they fight each other rather than Shinji having to fight), and the pretty countryside is a way to placate Shinji. Note also that, as time passes, Pokemon designs look more and more like Angels — would you be surprised if Deoxys, Palkia, or Regigigas attacked Tokyo-3?
Alternatively, the apocalypse mentioned in the first Pokemon theory above was Third Impact.
Alternatively alternatively, the entire show was made by people who had just watched the entire show through End of Evangelion and needed something to restore their sanity, but who couldn't get Evangelion out of their heads entirely.
Does this mean humans are the 494th Pokémon?
No, they're the "zeroth" Pokémon. (Which, one supposes, makes Missingno the negative first — or going even further, the ith Pokemon, which in some ways would be appropriate.)
Alternatively alternatively alternatively, it's an alternate universe where alternate evolutionary paths are in fact capable of coexisting. Pokemon are the Angels (great diversity of forms and odd powers being the sort of thing the Fruit of Life gives) and humans are human (technology given by the Fruit of Knowledge being their sthick). The reason why there are more Pokemon than Angels is that they cooperate with humans, lessening the selective pressures and allowing for greater genetic diversity.
Mew, as the progenitor of all (non-legendary) Pokémon is an Adam-type seed.
This gets even better when realises that in the manga the mysterious dark glasses wearing scientist (Blaine/Ikari) has an embryonic clone of Mew/Adam implanted into his arm.
All of this... I just can't deal.
I'm seriously laughing so hard I can't even cap it right.
