Breed a Sturdy Togedemaru with Encore (you can use Plusle or Minun as the parent, they get it at level 10 or something). Max out its speed to be in the safe side. Send it up first and use Nuzzle, followed by Encore to lock Kyogre into Surf. From here you can use a mon with Water Absorb or Storm Drain and take advantage of the couple of free turns you get to break shields. Something else will have to clean up, physical attackers preferred since the seed it starts with buffs its Sp Def.
You could potentially do other things, like transform the field with Blizzard, or lower its Sp Atk with enough Snarls, but I think the above takes the least overall prep time for how well it works.