Kyogre has supreme power, but it's extraordinarily predictable and only good for special attacks, so it can get walled when you're not careful.
With Mew, on the other hand, no opponent will have any idea what to do to defend against it until they test it out with Protect or Substitute or something similar. Even once they figure it out, it can still do mixed offense really effectively, or just hit Explosion as a last resort, so it's not like one Pokemon can stop it dead cold.