Pokemon used to be Science-Fiction. The most powerful legendary in gen 1 is Mewtwo- a genetically-engineered creature of science. We also have Mew, whose pokedex just mentions it being rare, and the legendary birds, who are pretty much just powerful and don't have any mythological associations at all in-game.

The only ghost types are identifiable with a man-made machine- they're Ghostbusters style "ectoplasm" ghosts rather than fantasy-style spirits. There are psychic types but no "magic" types. There were Pokemon like Magneton, clearly a robot-flavored being. Muk is said to be from "Sludge exposed to X rays from the moon." Starmie and Clefable are hinted to be from outer space. There's Jurassic Park-esque "reviving dinosaurs" stuff going on. Like, the science isn't remotely believable but it's definitely FLAVORED as a science-based world, and none of the Pokemon are really magic-flavored.

Starting with gen 2, the franchise shifts to fantasy. Ho-Oh and Lugia are ancient God-like creatures with temples built to them. The legendary beasts, too, have a mythological origin story, and Celebi is a deity-esque protector of forests. The plotlines starting in gen 3 all shift towards JRPG-style "summon an ancient god being to destroy the world" plots. Gen 6 adds the fairy type- fairies being explicitly magical beings. There's definitely still some more sci-fi dudes (genesect, beheeyem, fossils) but overall I feel like the franchise definitely shifted.