Mewtwo, Mew, Ho-Oh, Luigia, Celebi, Kyogre, Groudon, Rayquaza, Jirachi, and Deoxys are not allowed to be used in the Battle Frontier. If you try to enter them in a facility (or one of the three Battle Tents in Emerald), it will say something like "NOT ALLOWED".
Also, just kind of off-topic (but...