If you're looking to make Legendary battles more difficult, why not make them like the Totem Pokemon battles? Boost one or more of their stats and also have them summon another mon for help. For example, have Kyogre summon an Alomomola and (like with the Wishiwashi Totem) have it spam Heal Pulse and Soak. Or, like, I dunno, summon an Araquanid/Clawitzer/Dewgong/Luvdisc with Entrainment and give Kyogre any of their useful abilities.