When you get the Go-Goggles and defeat the Elite Four, catch a Trapinch in the desert. Keep it up the top of your party until you run into Latias. Trapinch's special abilaty is 'Arena Trap' which means the foe cannot escape. So if you used the master ball on Grondon/Kyogre you still have a chance. But make sure you train it to a high level like 70 so you can weaken it first.