Going by the lore, one could guess the differences between Rayquaza's Mega Evolution and a regular Mega. It evolved when the Church of Rayquaza prayed to it's savior before the Great Stone. It didn't have a trainer, a pratice only seen before in the movies by Mewtwo and Diancie. Diancie used a Mega Stone of her own creation and didn't require a Key Stone, while Mewtwo could spontaneously transform into it's MMY form with no requirements needed. The Great Stone could either be a Mega Stone or a Key Stone, but personally I would guess it's the Rayquazite. The method worked because Rayquaza Mega Evolved in the Stone's presence, most probably at Sky Pillar. In-game, that would mean Rayquaza could Mega Evolve when you battle it at Sky Pillar despite being a wild Pokémon (reacting to the prayers of the people suffering the effects of Desolate Land or Primordial Sea), then you grab a chunk of the Great Stone and give it to the dragon to carry around.