Also a thought: in a legendary village, cranky Rayquaza having to settle frequent spats between Kyogre and Groudon, particularly if they were allowed to have some weather-altering powers. It'd be fun chaos, lol. You could affect the weather by taking sides if you particularly wanted rain or something.
Because let's be real, the Emerald cutscene makes Rayquaza look so much like the cranky parent. xD Not sure what its bipedal form would be either, though...