I went to use the Battle Subway without enough Pokemon in my team and the guy said that some Pokemon were banned (Celebi, Deoxys, Reshiram and Kyurem). So I traded over Giratina and the guy then said Giratina was banned. So I'm guessing it just goes by who's in your Pokedex?
Terrakion and the other musketeers are okay, as is Tornadus. What are all the legendaries that are allowed?