You can't have Kyogre without Groudon, although honestly if both Pokemon are awake and wandering around some cataclysmic event is going down. Youtube user Pangamma created both in 3D, going so far as to hollow out both structures for ease of use.
He's also shared his schematics here, so you too can go forth and create your own Groudon in Minecraft. I wouldn't though. After replaying Pokemon Sapphire recently, I'm totally afraid that Groudon might be behind our current global warming.