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Applin aren't just based on apples, they're based on Leppa Berries (apple spelled roughly backwards) which in turn are based on crabapples (Grav Apple is a pun on crabapple).
Leppa Berries are stylized to have a yellow jagged underside. Applin has the same distinct yellow underside resembling teeth, as well as the two leaves serving as eyes. Someone over at Game Freak checked to see if they already HAD an apple to base this creature on, found out about Leppa Berries, and fashioned Applin after one.
