Mega evolutions are often characterized by the strong bond of people and their Pokemon. What I'm seeing here is that:
Kyogre and Groudon gain tremendous power from the sea and land, respectively. Because of the weather they cause, they also take some power from the sky, leaving Rayquaza a little starved. Kyogre and Groudon's designs suggest that, as implied by the term "Primal", they've gone 'blind' with their power (just look at their eyes) and want more of it for themselves (according to the lore on the official site, and also due to the more selfish mechanic of the primal weathers).
Rayquaza, on the other hand, gained power from the pitiful cries of the terrorized people and their pleas for help. Because of the strong bond, Rayquaza was able to Mega Evolve. In contrast to Kyogre and Groudon's "power hungry, steroid-filled, blind with fury" designs, Rayquaza's design is sleek and modern. It's a way of saying that Rayquaza is looking into the present situation and how it can stop the feud, whereas Kyogre and Groudon look into the past to gain more power for themselves
Of course, there could be an alternate universe where Rayquaza gets power hungry and regular groudon and kyogre must work together to stop it...