A phylogeny based on all current Pokemon. A few notes:

- I went with the idea that each Pokemon "evolutionary family" is one species, with each member of that family a different growth stage from the others. So, essentially, this is a universe where almost everything goes through metamorphosis (and can stop the process of metamorphosis if they or their trainers wish to)... Don't think too hard about it. For those with branched "evolutions", the final "evolutions" are close relatives of each other that have similar young (with the exception of Beautifly and Dustox, where the similarity between their larvae are the result of convergence).

- The phylogenetic positions of the Pokemon are based on their real-life counterparts. I had to make up new clades for certain Pokemon groups with no close living counterparts, notably the "ghost" clade for Pokemon based on ghosts, darkness, and inanimate objects (descended from amoebazoan-like organisms), the "rock" clade for Pokemon based on rocks, steel, ice, etc. (related to panarthropods), the "dragon " clade for Pokemon based on dragons or are vaguely reptilian but don't closely match any real-life reptile (closely related to dinosaurs; ancestrally bipedal), and a "legendary birds" clade for all those bird pokemon that don't match any real-life birds (also includes non-legendary birds such as Altaria, Togekiss, Xatu, Fearow, and Skarmory; incidentally, I made Articuno a weird polar trogoniform). Note the only real-life group whose phylogeny I'm actually familiar with is dinosaurs, and I apologize for the fact that some of these phylogenies are probably outdated. (Also, the phylogenies of many groups, such as mollusks, teleosts, neopterans, teleosts, neoavians, teleosts, teleosts, teleosts, as well as teleosts, are currently in a state of flux and have no consensus, and so are likely completely wrongly arranged here.) A word of caution: I relied mostly on superficial morphological similarities among Pokemon (especially for the made-up clades) and didn't take into account much else (such as stats, breeding groups, etc.) Including those in an analysis may result in an entirely different phylogeny, but I'll leave that to more hardcore fans.

- Persian, Delcatty, Purugly, and Liepard represent different breeds of the same species; same with Arcanine, Granbull, Houndoom, Smeargle, and Stoutland. Mothim/Wormadam, Combee/Vespiqueen, and Nidoking/Nidoqueen represent sexual dimorphism among the same species. Mewtwo is an artificially bred subspecies of Mew. The Porygon line, Deoxys, and the Elgyem line are entirely artificial or extraterrestrial Pokemon and therefore don't belong to the same tree as Earth Pokemon. (I decided not to mess with the idea that some other Pokemon have also been rumored to be extraterrestrials, such as the Clefairy line, the Staryu line, Lunastone, and Solrock.)

- In this interpretation, legendary Pokemon aren't literally deities, just particularly rare or powerful (or both) and therefore are shrouded in myth.

- I included Huntail and Gorebyss as fish-like free-swimming mollusks with young that resemble more conventional bivalves.

- Similarly, Octillery is a cephalopod with fish-like young.

- Bisharp is not specifically based on insects, but I thought that it kind of resembled an arthropod. I included it as an ant.

- Gyarados and Milotic are very, very large and derived carp and bass.

- I'm not wholly convinced that Lickilicky is a lizard, but I couldn't figure out where else to put it. In this phylogeny, it's a skink.

- Serperior is the most basal among the snakes due to the fact that it retains legs as a juvenile.

- Unfezant is a galliform with highly precocial, pigeon-like young capable of strong flight, similar to real-life megapodes. (In fact, young megapodes are better fliers than adults and can make sea crossings!)

- Venusaur is not a dinosaur. It doesn't remotely look like a dinosaur, and the "-saur" reference is something only present in the English names; the original Japanese only references the flower on its back and how freaking weird it looks. I've always thought the Bulbasaur line looked more like aberrant frogs myself. Some have suggested that they're dicynodonts, but I'm... still not convinced to say the least. So why the position as a basal synapsid? The external ears gave it away. (I also decided to make Nidoking/Nidoqueen basal synapsids for the same reason.)

- I went with Golduck being a platypus, and being most closely related to Ludicolo.

- I decided to make Slaking an aberrant sloth with young more similar to conventional sloths. It's more interesting that way.

- I just went with Shaymin being a hedgehog and decided not to think too hard about the whole forme-changing thing.

- Took a while to decide whether Kyogre was a whale or what. Stuck with whale in the end.

- Arceus is a horse. Yeah.

- Absol is a carnivoran not closely related to any other carnivoran group.

- Entei and Raikou are felids, while Suicune is a basal canid.

- Bulbapedia makes a decent case for Dewgong being a sirenian, but (especially given its "pre-evolution"), I still see it as more of a pinniped.

- Similarly to Slaking, I went with Samurott being a large, aberrant sea otter. More interesting that way.

- Exploud, Wigglytuff, Audino, Clefable, and Blissey are aberrant lagomorphs. Even Exploud, yes.

- If I were to make a new version of this I'd probably have Azumarill closer to Raichu than to Plusle and Minun.

- I know Mew is supposed to be a cat or whatever, but I... don't see it.

- Victini is a euarchontoglire closely related to Glires.

- Primates are far more diverse in the Pokemon universe than in ours, mostly because I shoehorned in most of the humanoid Pokemon as hominids.

- Disclaimer: The little Pokemon icons come from Bulbapedia and don't belong to me.

Edit: I've been informed that the Magnemite line, the Voltorb line, the Golett line, the Bronzor line, and the Regi trio are also artificial Pokemon, and I'd remove them from the main tree in an alternate cladogram, possibly along with the main Sinnoh legendaries and Unown. In hindsight, I should've also had Latios and Latias representing sexual dimorphism in the same species.

Update: Forgot the non-insect panarthropods earlier.