I think all of the real world references they make in the games (they made them especially in the original games and as such the remakes) kind of ruin the Pokemon mythology for me. Mew being found in South American is ridiculous, and Lt. Surge being an American, etc... All of the Pokemon games take place in made up regions of a nation and at this point are now featuring Pokemon that control space and time, Pokemon that helped create the universe (Mesprit, Azelf, Uxie), and a Pokemon deity (Arceus). Referencing the real world ruins this, because they're now making Pokemon practically a religion in the games. It ruins the fantasy.
See Final Fantasy games, Lord of the Rings, etc. for good examples of fantasy worlds. Pokemon doesn't cut it.