In the pokemon series, the trio of Groudon, Kyogre and Rayquaza both gained new powers after mega evolution was discovered, but why did Groudon and Kyogre get a primal form and Rayquaza got a mega, is it possibly because Rayquaza doesn't have a orb?
I've not watched the new Pokemon episodes or played the ORAS Games. So this answer is a culmination of research and not first hand information.
A google search lead me to a reddit where this has been discussed. Why Rayquaza Didn't get a Primal Form. I also read through several forums and blog post that led to "plot" and the "game story". However, one of the comments seemed pretty logical to me.
It's been stated that Rayquaza went Mega instead of Primal, because Primal means being in an anger driven state, only guided by instinct, which is why the Primals just try to seek for the most power possible while Mega Evolutions completely retain their state of mind.
According to the reddit,
We know that primal reversion is when Kyogre and Groudon revert to their ancient states in which they had even more massive amounts of power than they do now, but Rayquaza was not like them and had enough power to stop the primal forms even in its normal state. Zinnia provided this information in the Delta Episode while she is explaining the mural to you at the end of the story. She also says that when a large meteorite was going to hit the Earth, Rayquaza gained more power through the bond between it and the ancient people of Hoenn, i.e. mega evolution.
Read the player dialogue with Zinnia to understand more. The story told between floors enumerate this. This also gives insight into the actual Mega Evolution process, i.e. Rayquaza was the first pokemon to Mega-Evolve.
Source : Bulbapedia - Zinnia
It was humanity's wish that brought about Rayquaza's transformation in the face of the rainbow stone... Yes... A wish... An intangible thing, invisible to the eye. Yet this wish bound people and Pokémon together, enabling the Legendary Pokémon to change its appearance... Doesn't it remind you of something? That's right... It sounds like Mega Evolution, doesn't it?"
TL;DR Rayquaza in itself is more powerful then the 2 Primals who reverted to their ancient form in anger and more power. Rayquaza, however went Mega to save the ancient people of Hoenn from another disaster in a seperate event. BSTs hwoever disagree with this.
Base Stat Totals:
Rayquaza 105/150/90/150/90/95 = 680
Rayquaza-Mega 105/180/100/180/100/115 = 780
Kyogre 100/100/90/150/140/90 = 670
Kyogre-Primal 100/150/90/180/160/90 = 770
Groudon 100/150/140/100/90/90 = 670
Groudon-Primal 100/180/160/150/90/90 = 770