The Pokémon Company mentioned that the Pokémon on the box art were "never before seen Pokémon", the same expression used to refer to Kyurem's alternate forms and Mega Mewtwo Y when they were first released. This suggests Kyogre and Groudon will get either of the two treatments. Much to the dismay of uber players everywhere, I guess. Kyogre and Groudon don't need anything extra, dammit!
Still, I wonder where this is going. My personal theory is that regardless of what happens, they're going to get abilities which function just like Drizzle and Drought used to in gens 3 through 5. And while this would be a huge blow to an ubers metagame that somewhat freed itself of perma-weather's stranglehold to an extent, didn't it come across as sketchy to anyone else that Politoed, Ninetales and Mega Charizard Y could summon weather automatically in the same way those two super-powerful legends could? My bet is that they're trying to do something about that.