I've had a similar idea for Bulborbs being gastropods, my take on them is that they are descended from a form of secondarily-terrestrial sea slug that internalized its shell and evolved a pair of swimming fins during an aquatic intermediate. Over time, the internal shell became segmented and became similar to a pseudo-vertebrate skeleton, with one segment becoming part of the head as an "upper jaw" to hinge with a modified radula as the "lower jaw", while other segments migrated to the fins, forming jointed "legs" when it returned to a terrestrial lifestyle. In the eusocial Empress Bulblax, these legs are more or less atrophied, as well as being undeveloped in the early-stage Bulborb Larva.
Blowhogs as macro-tardigrades fits too well (they are after all just a few inches long but massive for a normally microscopic tardigrade) though they would probably keep the eight legs.
Dweevils most resemble harvestmen, but with only six limbs they don't look like arachnids. They're probably insects, and the four eyes are two compound eyes and two enlarged ocelli.
Snagrets are most certainly birds: likely a descendant of cormorants and other diving birds that developed fused legs much like a seal's fluke as they became increasingly aquatic and flightless. However, at some point, they returned to land, and adopted a burrowing ambush predator role, losing their vestigal wings and developing scale-like scutes from modified feathers as protection against the abrasion of soil and sand, though more typical feathers are retained on the head as display.
Pikmin themselves are as anon suggested quite sensible as an insect parasitized by a Cordyceps-like plant. But instead, it's a mutualistic partnership as opposed to a parasitic one (which may have been the case for the initial ancestral forms), so much so that the two have long co-evolved like with eukaryotes arising from ingesting smaller microbes that since became chloroplasts and mitochondria.
The insect in question is likely a eusocial hymemopteran, as the Winged Pikmin display transparent bee-like wings and are probably a basal form that other types which are more derived have since lost. The symbiont plant has taken over the insect's body, with a stem emerging from the head that produces food via photosynthesis and rootlets growing through the limbs that allow for the absorption of moisture and sugary nectar for nourishment. The insect itself has thus become very simplified, losing its mouthparts like mayflies and moths, but being sustained by the plant instead of dying after a few days, and the resulting appendages becoming specialized in different species: the Red Pikmin develop a sharp proboscis used for attacking enemies, the Yellow Pikmin modify their antennae into "ears" that act as gliding surfaces, and the Blue Pikmin repurpose their oral cavity and digestive tract into a makeshift gill for underwater respiration. Rock Pikmin deposit minerals into their hardened outer exoskeleton, making them very sturdy.
The Onion is a motile triradially-symmetrical plant that may be related to the Quaggled Mireclops. Similar to a fig, it bears fruit and flowers that bloom inside the outer bulb, with the Pikmin taking a role akin to fig wasps in aiding its pollination. Somewhere in its evolution, the plant's seeds began parasitizing its resident pollinators as a means to spread, but over time it became a mutualistic relation now with neither plant nor insect able to survive without the other. The life cycle thus takes place with the all-female insects laying eggs within the bulb, which hatch into larvae. The larvae are fed with food the adult Pikmin carry back to the Onion, but at the same time, they are implanted by the Onion's seeds. Once the seed begins to grow in the larva, it then pupates, is ejected from the Onion, and plants into the ground, and the pupa is the sprouts that the captains pull out of the soil to emerge as an adult Pikmin. Most of them spend their entire life as a motile insect-plant composite, but from time to time, given proper pheromone and hormonal signals, specialized Pikmin eventually have their plant component absorb the insect component which dies in the process, allowing it to metamorphose into a new Onion and start a new colony elsewhere.
The Hocotatians are likely bona fide aliens, given their inability to breathe oxygen. I picture them more as fuzzy tiny koala-esque creatures because that's the vibe I get from their character design. The "rescue pups" are likely aliens as well, though probably from a different planet than Hocotatians as they can breathe oxygen just fine, and here they have a more jerboa-eque build that better fits them being bipeds. Their good sense of smell, but lack of a visible nose, could suggest that what appear to be "ears" are in fact olfactory antennae capable of picking up scents in the air or on surfaces.