When catching rare pokemon like Grudon, Rayquaza, Kyogre, Latios, Latias, and many others, you do NOT have to use a master ball. What you do when you get to the area, say the Cave of Origin for example, save the game when you get to Kyogre or Grudon's lair, and have a variety of balls, mostly ultra balls. Have plenty of revives and potions. If you faint Kyogre, just restart the game and try again. This make take longer than using a master ball, but it does work. I have caught Kyogre, Latios, Rayquaza, and Latias using this technique. Just don't forget to save the game if you can!