How do you apply taxonomy to Pokemon when the fundamental unit (the species) has no clear definition? Reproductive barriers which constitute both the prevailing basis for the species concept and a key mechanism by which species diverge in the first place are extremely fuzzy in Pokemon. How do you define a species when each individual is capable of having viable offspring with hundreds of other radically different Pokemon? Darwinian processes that form the basis for the diversity we see in our own world won't work the same way in Pokemon. While there is evidence that some similar processes shape the way Pokemon have evolved (genes for example are confirmed to exist, but clearly function differently to our own), the mechanisms are unknown
and likely to result in a tree of life that is very different to the one we see in our own world.