Even so,where are the cats? the dogs?..they show Ash and Co. eating meat..Does that meat come from a pokemon or an actually animal like a cow or pig?If it does,then where are the cows and pigs?If there were any real animals they would have been shown in more than just one episode.
There was an Animanga scan showing some sort of Japanese-esque festival with Misty, Ash, and Brock in those Kimonos and it also had a dog on there. I'd post it, but unfortunately, BMGf is currently experiencing technical difficulties so I can't.
For other examples, Misty mentioned "Bottom-feeders" such as catfish in an Orange Island episode.
Lion tamers were referenced in the A.J. episode.
Pidgeotto was seen eating a worm at one point of the show.
in the 9th Pokemon movie, there were several shots of coral reefs (yes, coral do count as animals, because the taxonomy of biological animals listed them as such)
A starfish was seen as well, if I recall correctly.
Gastly transformed into a Mongoose at one point.
I think there was a stall of freshly caught fish in the Beauty and the Beach episode
There was a Lobster on the St. Anne
the swimming fish scene was both in Pokemon Shipwreck and Waterflowers of Cerulean City.
and possibly more examples thant I can't think of right now. Plus, in the Japanese version, they still keep cricket/cicada sound effects even when they can just as easily change them to their pokemon counter parts.
also, Rayquaza DID kinda place an entire city with innocent bystanders in grave danger when it was trying to fight deoxys.
also, considering how a Wailmer was seen in Johto, the Keckleon bros. appearances in Johto, and Latia and Latios being protectors of a Johto territory known as Alto Mare (Not to mention that the 9th movie was near Johto if the official maps mean anything), I'd say that it's extremely likely that the 3rd gen pokemon (maybe even 4th gen pokemon, if Pokemon such as Buizel, Mantyke, and Manaphy mean anything.) are ALSO native to Johto.