Some legendaries will be (surprise, surprise),
version-exclusive:
Ultra Sun: Ho-Oh, Raikou, Groudon, Latios, Dialga, Heatran, Reshiram, Tornadus, Xerneas,
Ultra Moon: Lugia, Entei, Kyogre, Latias, Palkia, Regigigas, Zekrom, Thundurus, Yveltal,
Both: Mewtwo, Zapdos, Moltres, Articuno, Suicune (needs both Raikou and Entei), Rayquaza (needs both Groudon and Kyogre), Regice, Regirock, Registeel, Giratina (needs both Dialga and Palkia), Uxie, Mesprit, Azelf, Cresselia, Kyurem (needs both Reshiram and Zekrom), Cobalion, Terrakion, Virizion, Landorus (needs both Tornadus and Thundurus), Zygarde