One thing I've been wondering for some time now is whether Pokemon as a whole can be called a kingdom or even the more or less recent rank of domain. A domain is higher than a kingdom and there are two or three depending on who you ask (either Archaea, Eubacteria and Eukaryota or simply Prokaryota and Eukaryota). Pokemon seem to be different enough from animals that they would not be classified as part of the Animalia kingdom, but I'm not sure if Pokemon as a whole can be considered one kingdom.
The main reason I think this is because of Grass-type Pokemon, as well as the many inorganic Pokemon and Ghost-types. The cells of plants are different from animals, and likely Grass Pokemon cells are different from animal-like Pokemon. Perhaps they're different enough to be considered a different kingdom all together? What about Pokemon that seem to be both plants and animals, would they be a separate kingdom as well?
I personally think of Pokemon as a Domain. What makes Pokemon different from any other Domain is their ability to use special Moves as well as most Pokemon species' ability to undergo a rapid metamorphisis, or what we call "evolution". It is perhaps more related to the Doman Eukaryota (protists, plants, fungi and animals) than Archaea (very simple bacteria, believed to be among the vbery first lifeforms) or Eubacteria (most other bacteria), but it is it's own separate Domain. Biological classification is based on similarity in gentics as well as a common point of ancestroy. Since "all" Pokemon possibly descended from Mew (though I believe this is only regular Pokemon and perhaps some of the Legendaries),this is the common point for Pokemon.
Of course, trying to classify Pokemon using the taxony used for life in the real world can be tricky. For example what about the whole Pokemon being able to bred with other species so long as they are part of the same Egg Group? Being able to bred and produced viable offspring with each other is a big indicator of being part of the same species. Does this mean that all Pokemon of the same Egg Group are actually one species? If Pokemon biology were more like real life organisms, then Pokemon interbreeding would produce some form of hybridization rather than the baby being the same species as its mother. What do we make of this?
Well anyway, that's just my theory. What do the rest of you think?