so, how about this: when we are battling, we dont know it at the time, all we know is tha it is a "big green pokemon" and we go inside. the news is on, and sightings of a big green pokemon belived to be rayquaza have been seen throughut the world. and then, the news explains the story of rayquaza told in r/s/e. how does that sound? of course, its not the actual written part, its just a summary of what it might be.