I originally thought it'd be a problem, but... Lexifox posted...
Doesn't this not really matter since most of the time you have access to larger Flying Pokemon when you get the HM?
exactly. If I don't have a Flying type on my team I usually teach Fly to a Pidgey, Starly, Pidove that I caught on the first route, but they could easily fix that by making a common bird that was larger. Anyway, it encourages people to have at least one decently leveled Flying type, so that's not a problem at all.
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