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With Kyogre at least humanity might have a chance with a Water World scenario, not to mention a bunch of Pokemon types could adapt to an ocean world, especially Water and Flying.
With Groudon everything will just flat out die. No survivors, not even those of Groudon's own fucking type. I can't imagine Fire, Rock and Ground don't need at least a little bit of water.
I'm still picking Groudon though.