In sorting a phylogeny based primarily off of egg groups, I decided to look at members of the Bug group first. It's a relatively small group, and a lot of the members are unambiguously based off of actual organisms. There are a number of issues, though, which I'll ramble on about at length below; brace yourselves. But first, here's our tree:
How the subphyla of arthropods are related to each other is still a subject of some debate. I'm running with the prevalent scheme that divides arthropods into the clades Mandibulata (including insects, crustaceans, and centipedes and millipedes) and Arachnomorpha (including arachnids and horseshoe crabs). Let's start with the mandibulates.
The majority of the Bug group's members resemble insects. Scolipede, which seems to work fine as a centipede, is rather lonely as the sole representative of Myriapoda.
I was surprised to not find any crustaceans in the Bug group. (Kingler and Crawdaunt are in Water groups.) "What about Crustle?" you say. "That's a hermit crab, yes?" I have some weird ideas for that one -- just hold on until we get to the arachnomorphs.
Also, wow, are there no Pokémon based off of flies?
Most of the insect Pokémon neatly work as parallels to real insects (Yanmega's a dragonfly, Beedril's a bee...), so I arranged them according to current phylogenetic hypotheses. There are a couple of more obscure species worth pointing out, as well as parts where I had to invent a fair bit:
Dragon-like, but not a dragon. And it's not a dragonfly. It's a highly derived lacewing (look, these ones are Flygon-colored!). Observe that Trapinch is definitely based off the antlion, the lacewing's kind of frightening larval stage.
If you compare the Red and Blue sprites for Venomoth's and Butterfree's lineages, the theory that their sprites were accidentally swapped makes a lot of sense. If Venonat evolved into Butterfree, I would propose that it does not belong with other butterflies and moths but is instead an oddly butterfly-like insect more closely aligned with hemipterans (true bugs, e.g. cicadas). This is based on Butterfree's biting and sucking mouthparts for feeding on tree sap, as well as apparent incomplete metamorphosis (no pupal stage). But they gave us Caterpie->Metapod->Butterfree and Venonat->Venomoth, so we'll have to run with that. Butterfree will just remain a butterfly with weird, biting mouthparts (which we can treat as a case of neoteny).
Looking at all the lepidopteran-like Pokémon, we find that Volcarona has a similar lifecycle to Venomoth, so at least they can be together in a clade. But I find it unlikely that anything within Holometabola would revert to hemimetabolism, so I put Venomoth and Volcarona as lep-like hemipteran things for now.
Note that Forretress and Wormadam/Mothim don't have pupal evolutionary stages. So are they hemimetabolous too, then? No -- as they are based on bagworms, trainers don't see the pupal stage because it occurs within the constructed case. And Forretress is unusual in that both males and females remain in their cases through adulthood; Wormadam/Mothim more closely reflect existing bagworms.
Genesect is a cybernetically (and perhaps genetically) enhanced prehistoric insect. Cool. Morphologically, that insect resembles Pokémon interpretations of mantids (Scizor) and phasmids (Leavanny) enough for it to plausibly fit in a nondescript sister group. There's not much to further define it. Any ideas?
Almost all of the species in our insect phylum analogue breed exclusively within the Bug group. There are some exceptions, though. The fact that Volbeat/Illumise also breeds in the Humanshape group is pretty troublesome, as the mammalian Humanshape group will end up very far removed from the Bug group. For the time being, I decided to just ignore that and assume they're fireflies with people faces. (I'd love to hear some ideas on how to resolve this oddity.)
Chelicerata consists of arachnids (spiders, scorpions, and some more obscure creepy crawlies) and merostomates (horseshoe crabs, extinct sea scorpions). We will see some Merostomata representatives in the Water 3 group. Within the Bug group we find arachnids. Ariados and Galvantula are straightforward enough as spiders. What else is in there?
Gligar and Gliscor have always been weird as Ground/Flying typed scorpions with bat wings. There's likely some inspiration from scorpionflies in there. Those are insects instead of arachnids, so named because the males of some species have scorpion stinger-shaped genitals. While that's fairly disturbing in its own right, I prefer to think of Gliscor as a true scorpion that has independently developed flight in the form of bat-like wings. You thought it was bad having to deal with brown recluses in your basement?
I also really like the phenotypic similarities between Drapion's and Gliscor's lines that seem intentional (see the tail, claws, fangs, segmentation, and color). Convergent evolution could explain away the similarities as well, but for now I say they're both scorpions.
While the acquired shell is obviously inspired by hermit crabs, Crustle is part Bug type and in the Bug group, unlike the other Pokémon crustaceans (Kingler, Crawdaunt). It is found in a desert climate, unlike terrestrial hermit crabs, which need to keep their gills moist. The thin flagellum at the end of its abdomen, used to hold onto the rock, looks similar to what vinegaroons have. Vinegaroons, however, don't grab onto rocks with their tail; they spray acid from it. Crustle doesn't do this, but Dwebble is described as expelling an acid from its mouth to aid in shaping its chosen rock.
You might have noticed that Masquerain and Shuckle are removed from both the mandibulates and chelicerates. Let me explain.
To me it looks like a slime mold that took up residence in a barnacle. Maybe a bizarre fantasy mollusc. But it's in the Bug group, and only the Bug group. I don't know.
Then we ask...
Similarly to Shuckle, it just doesn't really look like anything. Alright, Surskit is heavily inspired by a water strider, sure. But Masquerain? What is it? It has enormous wing-like antennae with eyespots and flies with its four paddle-like limbs, positioned beneath the body. Nothing looks like that.
But then notice how both Shuckle and Masquerain have four limbs, appear soft-bodied, and secrete sweet fluids in some stage of life (no, really, Surskit does this). So I propose that Shuckle and Masquerain represent an ancient clade that is sister to the rest of the arthropods, which diverged prior to the advent of chitinized segments and developed its own method of flight.