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This page serves as a general explainer on my reasoning and choices I made in categorizing Pokemon in this way. It is likely going to include large swathes of rambling to explain relatively simple points.
All Pokemon belong to the kingdom Sinummonstria, much like how all animals belong to Animalia. An argument could be made to separate them into Kingdoms following animal, plant, fungi, etc, but my counter-argument would be that all Pokemon share enough characteristics that they can be grouped together this broadly, and that this simplifies things considerably (in other words, I wouldn't have to think of as many names further down the tree). This would also imply that all Pokemon are Eukaryotes, which I believe can be easily assumed except in the case of those without physical forms (eg, most ghost types). In their case, the assumption of eukaryoticism is again made for ease of classification; if semantics are to be held, simply move the phylum Phantasma into its own domain - perhaps even making Phantasma the domain itself.
The phyla were decided based on the three overall broadest types of Pokemon design as well as their respective (usual) Egg Groupings. Creatura contains the Egg Groups to which Pokemon resembling existing forms of life belong (as well as Ditto for its relation to Mew and Mewtwo), Inanimata contains mainly the Mineral Egg Group and therefore encompasses most Pokemon based on inanimate objects, and Phantasma contains mostly the Amorphous Egg Group (and ghosts which belong to other Egg Groups) to cover those without physical form. There is a sort of priority taken when a Pokemon has two conflicting Egg Groups: a Pokemon with one Egg Group belonging to the umbrella of Creatura will likely be found in Creatura (except for those also belonging to the Amorphous Egg Group, which may or may not belong to Phantasma); a Pokemon with one Egg Group being Mineral and one being Amorphous will likely be found in Phantasma. For Pokemon belonging to the No Eggs Discovered Egg Group, phylum classification is decided on a case-by-case basis using mostly morphological criteria.
Some exceptions exist for each of the criteria. For one example, see below, "Special Case: Corsola and Cursola."
The adult (see below, "Species") is the Pokemon which is used to determine Egg Grouping, with some exceptions.
Class is determined primarily by specific Egg Grouping for the Creatura phylum. Here I am faced with a problem - does Egg Grouping more strongly relate ancestry than body plan? In the real world, creatures of different species don't typically interbreed, in fact, that's how a species is often defined. In the Pokemon world, however, any two creatures sharing an Egg Group may interbreed. The real problem arises when you get a Pokemon which is obviously based on one species that is in a completely different Egg Group to a Pokemon which is based on a similar species that, in real life, would be in similar categories. For example, take the Krookodile line (Domoris odosu), which is in the Field Egg Group and Feraligatr (Mordices ago) which is in the Monster and Water 1 Egg Groups. Both are clearly crocodilian, but they have vastly different interbreeding capabilities.
You may disagree with this decision, but I chose to use the Egg Grouping as primary deciding factor in where to place a species as interbreeding seemed, to me, like a clear indicator of closer genetic ancestry than body shape. This does imply that some members of an Egg Group have evolved "against the grain," so to speak, such as a member of the more mammalian-dominated Field Egg Group convergently evolving feathers or scales.
To further complicate things, Pokemon often belong to two Egg Groups. A further system is therefore in place to determine Class (in order of priority):
So a Pokemon in the Field and Flying Egg Groups would belong to the Ascella class, while a Pokemon in the Field and Water 2 Egg Groups would belong to the Capillia class.
For the other phyla, class is usually morphological.
Order, Family, and Genus are determined much by morphology, and often the presumed diet and Egg Group where applicable. Each level focuses on more specific features of body plan.
Species is determined both intuitively and not; in general, a species is determined as the collection of a specific evolutionary line (here used in the in-universe sense, not the Darwinian), with the final stage(s) being referred to as the "adult" of its line. Each Pokemon with an entry in the Pokedex is NOT its own species but does belong to one. The driving force of this decision is that, in the traditional sense, a member of one species does not transition into a member of a separate species as it matures.
I tried to develop species (and subspecies) names using the language of the area to which the Pokemon is native (first 4 gens = Japanese names, gens 5 and 8 = English or Latin, gen 6 = French, gen 7 = Hawaiian, gen 9 = Spanish), but like everything else there are exceptions. I made the unwise decision to use Google Translate for this, so if you see a word which definitely does not mean what I say it means, feel free to suggest a better one!
In some cases - namely regional variants and split evolutionary lines - a species will have at least one subspecies. Which is determined to be the subspecies depends on which was extant first, that is, the first to exist is the more general species while the new form is the subspecies. For example, the Alolan Ninetales line is a subspecies of the Ninetales species, and so gets a subspecies name.
The rule of thumb: if a Pokemon can change between forms freely (as in, with an item or status condition), then the forms will NOT be listed as different subspecies. If the alternate form cannot be freely changed into/out of (as is the case with regional variants), then it WILL be listed as a different subspecies.
In the case of widely branching evolutionary "lines," the most mature non-split form will be labelled the base species, while the branching evolutions will be given subspecies status. In the case of Eevee, for example, Eevee (Alepou shinka) is the species, while Jolteon (Alepou shinka fulgur) and Espeon (Alepou shinka sensus) are two subspecies.
Corsola and its Galarian form and evolution are a relatively unique case wherein a single Pokemon is classified as two vastly separated species (going so far as to be placed in different phyla, even). This decision is based on the fact that the Cursola line is implied to be the spirit of an ancient Corsola, rather than a living Corsola itself, and therefore its placement in Phantasma as a separate species is warranted.
Typing is not a major factor in the classification at any level because it is mostly irrelevant to the relatedness of Pokemon and their interbreeding capabilities. To demonstrate, Electrode (Genus species) and Minun (Pikachu negativus) are both Electric types but belong to two different Egg Groups, while Arcanine (Skylos kasai) and Samurott (Lutra samurai) are completely different Types but belong to the same Egg Group (Field).