Generation I - Kanto
Generation II - Johto
Generation III - Hoenn
Generation IV - Sinnoh
Shaymin (Sky Forme)
Generation V - Unova
Generation VI - Kalos
= 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.