Actually, I was playing Blue Version today, and guess what I stumbled upon ?
Several references to NORMAL animals.....Whoda thunk ?
There are real-world references throughout the Pokemon franchise.
The Pokedex info, usually the "species" type, often compares a Pokemon to some type of animal, either living, extinct, or mythological/fictional.
There is no shortage of references to real-world places. The United States, China, and the South American country of Guyana are all countries that are directly referenced. The anime, video games, and manga have multiple cities, towns, and sights that certainly resemble real-world sights too.
And yes, some animals are seen in the anime, usually in the early seasons. Coral is seen in the Manaphy movie though, and "Sounds of Nature Track 01- Birds in Forest" can usually be heard in the background of most anime episodes.
Why don't we see them more often? The show is called Pokemon. That's the focus, not the boring crap around it.