This answer has been in my head for a long time but I know that this answer is incorrect because in the movie, Destiny Deoxys, Deoxys had two opportunities to defeat Rayquaza. In the first battle, its vision was blocked by electro magnetic fields, and in the second battle, it was interrupted by the other Deoxys. So regular Rayquaza doesn't stand a chance against Deoxys, but mega Rayquaza does. Even then, in pokemon generations episode nine the trainer caught Deoxys and there wasn't a full-out brawl like the movie, but the episode is a direct reference to Pokémon Omega Ruby and Alpha Sapphire when you go to fight Deoxys in space, in which Deoxys was level 80 and could one-shot Rayquaza with its best attack (I forgot the name of the move). But it just shows how powerful Deoxys is and proves it is even stronger than Rayquaza.