Well, it'd be a combination of factors:
>rare in the wild or only common in a very small, secluded location (no zubat)>not considered especially dangerous to man (no sandygast or deino lines)>pokedex entries or lore does not mention a relationship with humans (no tropius, bruxish, turtonator, drampa, or delibird, despite their rarity)>not a special circumstance (a pokemon from thick jungles like sceptile would be unheard of if it wasn't a starter; Alolan exeggutor, despite only being found on one tiny island, is something of a mascot of Alola; fossils are obviously very strange; jangmo-o is rare but its final form runs an island trial; milotic is rare but well-known, etc.)This leaves a handful of pokemon like tangela, lickitung, jynx, dunsparce, wobbuffet, beldum, carnivine, maractus, tynamo, cryogonal, dedenne, noibat (?), and dhelmise, and obviously what
>>34732399 mentioned, with some exceptions like the revered rayquaza and the tapu.
Tell me if I missed any.