I would have to say groudon because there is nothing that can stop that massively huge Pokémon. I mean a Pokémon with that much power I mean come on guys seriously you think that kyogre can beat groudon I think not!! So I am casting my vote for Groudon.
Kyogre just because he is so insane. I like Groundon a bit but I think that fire and that is it is just asking to get killed by water. Water is far more versatile in my opinion. Plus I can ride on Kyogre in the water! How is that for versatile.
It actually depends on who sends out their PKMN first. If kyogre gets sent out first, Groudon will win. If the other way around, kyogre will win, since Groudon's Ability and Solarbeam combination will anhiliate Kyogre, and Kyogre's ability and hydro pump combination will obliterate Groudon.