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Maybe you should put it to sleep before it can rest? and i suggest taking an ice type with you (Regice or Glaile) and then try to capture it, or if the battle takes a while for ya maybe you should pack a Timer ball or 5 XD
Go and get a Pokemon with False Swipe. Better yet, get a Shedinja with False Swipe. Rayquaza only has one move that can hurt Sheddy and that's Fly. But you can bypass it by using Protect each time it flies up. You should read the FAQ first.