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Flygon should not be Bug Type. Not because Bug is unfitting, but because Ground and Dragon are both WAY more pivotal for Flygon thematically/conceptually. It's based on the "sand dragon" nickname antlions have. That pun is the entire basis on which Flygon was made.
Both of its current Types are MUCH more important than Bug Type for it, especially because Flygon is a reptile that merely resembles an insect. (the compound eyes, antenna and elytra wings all only superficial resemble insect body parts.) Don't get me wrong, Flygon still WOULD be Bug Type if having 3 Types was a thing, but without that, you clearly can't remove Dragon, since that's what it is. And you cannot take away Ground Type from it. The Pokedex literally calls Flygon the "elemental spirit of the desert". Trapinch burrow and dig traps in sand, Flygon causes sandstorms whenever they fly. Sand Tomb was originally based on antlion sand pits before it got changed to a generic sand twister attack. Everything about this family line is based around sand, digging and deserts.
The whole point of Flygon is being based around the "sand dragon" term taken literally, and its Typing reflects this. There just isn't any room to slap Bug Type on it while remaining faithful to what Flygon actually is conceptually.