If you think Rayquaza is the problem, I have bad news for you, TC. At least you can save before it and it's an interactable Pokémon. The Latis on the other hand roamed around so, they're hard to even encounter. Much more worthy of a Master Ball. At least they won't rest but, I think they have refresh in that game. Mean Look and Shadow Tag may help. Maybe you can manage to figure out the clone glitch at the Battle Tower and migrate a bunch of the legendaries over to your NDS games (if you have an original or NDS Lite).
AND NOW IT IS YOUR CONFUSION THAT SHALL BE THE ARK THAT SUSTAINS MEH!!!!!!! Random_Ghost to Tgirl