Put em to sleep so they don't rest... Try someone with False Swipe.. If u have Sceppy your in luck. Then its just Patience. It took me 4 hours of hunting to catch Latios without a Masterball man that was hell
master balls aren't everything. you will totally freak out with rayguaza if you don't get over that. buy 30 ultra balls, weaken it, paralyze it (not with thunder wave) and just keep chucking balls. you'll get him, eventually.
I just put kyogre to sleep and weakned it with false swipe. caught it with my fist ultra ball lol. same with groudon 'sept I froze him and he took me around 45 ultra balls. wish I brought along some timer balls...
use ultraballs if you were anygood at pokemon you wouldn't need a masterball in my emerald game i caght rayquaza in an ultra ball by using a level 58 breloom to use spore and then return it took me a couple times but i caught it in an ultra ball eventually and the same goes for latias i used wobbuffet as the 1st member of my team so it couldnt rub away.