PokéBase - Pokémon Q&A
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Best answer

http://bulbapedia.bulbagarden.net/wiki/Battle_Subway#Banned_Pok.C3.A9mon

Mewtwo, Mew, Lugia, Ho-Oh, Celebi, Kyogre, Groudon, Rayquaza
Jirachi, Deoxys Normal Form, Deoxys Attack Form, Deoxys Defense Form, Deoxys Speed Form, Dialga, Palkia, Giratina Altered Form, Giratina Origin Form, Phione , Manaphy, Darkrai, Shaymin Land Form, Shaymin Sky Form, Arceus, Victini, Reshiram, Zekrom, Kyurem , Keldeo, Meloetta Aria Form, Meloetta Pirouette Form, Genesect, and EGG

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going to edit this to be more neat in a sec..
Should I edit this with sprites?
Lol... "and EGG"