Prehistoric crustracean with gills which later become insect wings after it evolves and loses water typing.
Prehistoric bee and tree which both only evolve once they’ve interacted with each other.
Crustacean with one mid-section body segment which evolves into a similar crustacean but with more and more body segments each time.
Clam with light-sensing eyespots which becomes a squid with full image-seeing lensed eyes Even though Goodra sort of does this and it went over /vp/’s head
Ice type lizard which becomes fire type bird.
Boneless fish that evolves into a bony fish where the only bone move is related to calcium storage (maybe it heals status effects or eliminates stat reductions), then gets a proper skeleton with legs when it battles with that move on land.
Puddle of mud with lightening rod that doesn’t learn any attacks; when hit with an electric move in battle, it then evolves into a puddle full of virus-like mRNA bundles. Dex lore links it to Pokérus.
Lizard with legs which evolves into a legless lizard and gets a speed buff.
Fungus which starts out as a small mobile blob but evolves into a stationary structure sticking up out of the ground, implied to be interconnected to others which are too far away to see by underground hyphae. Maybe make it look like a radio tower to really drive home that it’s communicating with other units of the superorganism.
Tough looking beast wolf with high attack which evolves into small lapdog with high defense or lean doggo with high speed. Wolf prevo is still highest attack.
Tree Pokémon with dry skin, which evolves into burnt wood after being hit by a fire/electric attack, which then evolves into very high HP/Def/SpeDef Pokémon but is clearly a different tree with a notable layer of ash around its roots.
First dolphin Pokémon, which evolves from a bear-like creature.
Monkey with a club which becomes a knight with a sword which becomes a purple-haired hipster drinking a onions latte.