There are certain Legendaries that can go in, but most are banned. The banlist is:
>Mewtwo, Mew, Lugia, Ho-Oh, Celebi, Kyogre, Groudon, Rayquaza, Jirachi, Deoxys, Dialga, Palkia, Giratina, Phione, Manaphy, Darkrai, Shaymin, Arceus, Victini, Reshiram, Zekrom, Kyurem, Keldeo, Meloetta, Genesect, Xerneas, Yveltal, Zygarde, and Diancie
So basically any cover Legends and all Event Legendaries. The Legendaries that can get in are:
- The Swords of Justice – Cobalion, Terrakion, Virizion
- The Three Genies – Tornadus, Thundurus, Landorus
- The Legendary Birds – Articuno, Zapdos, Moltres
- The Lake Trio – Azelf, Uxie, Mesprit
- The Legendary Dogs – Suicune, Entei, Raikou
- The Regis – Regice, Registeel, Regirock, Regigigas
- The Eon Twins – Latios, Latias
- Standalone Legends – Heatran, Cresselia
I'm pretty sure I got them all.