Pokémon ecology, for the most part, seems to have usurped the niches found among animals in our world. We have birds eating worms and rats, mongoose chasing snakes, big fish eating little fish, etc. However, the elaborate abilities of Pokémon have caused an enormous change in global ecology. This essay will attempt to show the scope of the change.
There are real animals in the anime. However, they are very rare, except in watery scenes like oceans or seas. We only recall seeing the mongoose (an illusion cast by a Gastly) and some random tropical fish. This would make a great deal of sense, since the vastness of the oceans could enable some animals to stay away from their powered-up intruders (or relatives, whichever term you prefer). Surely, whichever "real" animals still exist only do so in pocket areas of the globe (unless Pokémon only exist in certain regions, but given the nature of their, especially the legendaries', abilities, that seems unlikely). After all, an electric eel can give you a nice shock that hurts, but a Pikachu or Zapdos can light up an entire city with continous arcs of electricity. "Real" animals would not be able to compete.
All is not lost, however. We suspect that Pokémon such as Rattata, Taillow, Sentret- indeed, most Normal-type Pokémon -are actually altered versions of "real" animals, by Mew or some other means. So, like dinosaurs changing into birds, these animals were somehow updated yet managed to keep their general identities. It beats extinction.
We assume that the legendaries came first (although perhaps they appeared the same time as the now-fossilized Pokémon), although it could be possible that some Pokémon later evolved into these highly powerful forms. However, human memories of Pokémon deem the legends as the most ancient, so we shall continue to hold the first view. These Pokémon, taken primarily from exotic human mythologies, also have the most power. All Pokémon myths seem to agree that the creation of the legends was a frightening time for both humans and non-humans. Despite all human efforts to control nature, to these beings warping reality was breathtakingly easy. Hurricanes, forest fires, earthquakes, lava flows- all these natural disasters soon became caused. Nature became the puppet to sentient beings, who, like most deities, were given to smashing and creating based solely upon their whims. However, Mew was not finished with creating, so animals were either replaced with more powerful Pokémon, or were transformed into Pokémon, creatures that, according to Mewtwo Returns, can more easily survive dramatic weather and climate changes.
Nature is a very single-minded thing; it does not require a multitude of solutions to various problems. It merely hones particular skills and anatomies, determining the best fit as measured by increased species population, and sticks to a rather limited movepool or body type. Thus, a robin eating an earthworm is replaced with a Pidgey eating a Caterpie or Weedle. A crocodile snatching a wildebeest is replaced with a Totodile catching a Tauros. A kangaroo is replaced with a Kangaskhan, etc.