PokéBase - Pokémon Q&A
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All Megas(Minus Blaziken and Lucario)
Porygon2
Burmy(Sand and Trash Cloak)
Porygon Z
Manaphy
Arceus
Victini
Deerling(Autumn and Winter)
Klang
Cobalion
Virizion
Terrakion
Kyurem(All Forms)
Keldeo(Both forms)
Chesnaught
Litleo
Pyroar
Floette(Red and Orange)
Florges(Red)
Honedge
Duoblade
Aegislash
Clawitzer
Carbink
Phantump
Yvetal
Zygarde
Diancie
Hoopa(Both formes)

Note: Does not include Movies and Specials, only Anime.

Source: http://bulbapedia.bulbagarden.net/wiki/List_of_Pokémon_by_anime_debut

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Mega Lucario and Mega Blaziken had already appeared.
Mega Blaziken when he saved Ash from meeting his demise when falling off Lumious tower and Mega Lucario under Korrina
Not entirely up to date on XY anime >.> but ty
Didn't Arceus appear in a Sinnoh movie? Don't tell me what happens I didn't see it yet. And also, Xerneas and Yveltal appeared in the movie: Diancie and the Cocoon of Destruction.
I put that in the note on the bottom that this is only the anime
Xerneas already showed up when Team Froakie and Team Squirtile were racing. This was anime.
I knew he appeared but i couldnt find the episode ;-;