The Pokemon world is basically our world, but with Pokemon. 

Every plant, animal (yes, they just aren't shown much because Pokemon are the main focus), fungus, protozoan, bacteria, and archaea alive on Earth today also exists in the Pokemon world. I don't see why animals wouldn't be in Pokemon if plants and humans are all over the place. Pokemon can eat real animals, and all of the normal Earth living things. Pokemon do compete with the real animals, but less than anyone would expect.

For geography, it's basically the same as our own world, with places renamed and some different construction. Though Game Freak has yet to discover most of it, only some of Japan, New York City, France, and Hawaii have been discovered so far. And because of the diverse terrain of this Earth, there are likely thousands of undiscovered Pokemon species in never-before-seen regions, maybe the Fakemon can fit in there. There are possibly more species of Pokemon than even shown in those already discovered regions, due to the anime and games having limited space. 

The natural history of the Pokemon world is also very similar to that of Earth, with very similar geologic time periods (like a Pokemon Mesozoic), and these geologic time periods hold even more undiscovered Pokemon. Think about it, 99.9% of all species on Earth are extinct, yet only a few Pokemon are really modeled off prehistoric animals. We don't have much Pokemon based on prehistoric Cenozoic animals or prehistoric Paleozoic animals, where are they? 

The myths of Arceus and the Creation Trio creating the Earth are probably just myths, believed by many, humans coming from Pokemon is likely a myth too; but they generally are widely believed. The technology of the Pokemon world is possibly even more advanced than on Earth, but not to the point where something can cure all Pokemon or like organ transplants for all Pokemon, though that's going to be a possibility very soon in their timeline.