Yes, Thundurus can be used in the Battle Subway. The only Pokemon that can't be used are Mewtwo, Mew, Lugia, Ho-oh, Celebi, Kyogre, Groudon, Rayquaza, Jirachi, Deoxys, Dialga, Palkia, Giratina, Phione (awwww. But everybody wants to use Phione), Manaphy, Darkrai, Shaymin, Arceus, Victini, Reshiram, Zekrom, Kyurem, Keldio, Genesect, and Meloetta.
