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This has been asked before, but in 2012, so I think I'm good to ask again.

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Generation I - Kanto

Charizard*
Butterfree
Scyther**
Gyarados

Generation II - Johto

Ledyba
Ledian
Natu
Hoppip
Skiploom
Jumpluff
Yanma
Gligar
Mantine

Generation III - Hoenn

Beautifly
Masquerain
Ninjask

Generation IV - Sinnoh

Mothim
Combee
Vespiquen
Mantyke
Yanmega
Gliscor
Rotom-Fan
Shaymin (Sky Forme)

Generation V - Unova

Archen***
Emolga

Generation VI - Kalos

Vivillon

= Only in the original Gen I games.
= This may be because it's evolution isn't a flying type
= It's this Pokemon's gimmick

Now that's all of them. As you can see, most of them were in Generations II and IV, with considerably less in Generations V and VI. If I missed one, let me know in the comments :)

Source: A lot of Pokedex page checking, and some experience.

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Scyther wasn't Flying-type in Gen 1? Interesting!
It was flying type, but maybe the Gamefreak staff were extrasensory and knew about Scizor before they started doing generation II.
Also, Doduo can learn fly.
Game Freak used Extrasensory! It's super effective!
you forgot charizard,it did not learn fly in red and blue
The question stated "As of ORAS", but I suppose I can add that in.
if you really want to get technical, Dragonite is under the same condition as Charizard in this context
Not many people remember that Zubat and Golbat didn't get Fly until all the way out in Gen 4 :c