Serebii has the lore for why quaza megas when the other two are primal.
It was a primal age, early in the world's history... The natural world was overflowing with energy. That energy granted Groudon and Kyogre an overwhelming power. Seeking ever more of that energy for themselves, the two clashed again and again, and their battles cast the people and Pokémon of Hoenn into great danger. Brimming with the overwhelming power granted by the energy of nature, this transformation was named by later people "Primal Reversion." And the people called their tormentors Primal Groudon and Primal Kyogre.
One Pokémon looked down upon this battle from the sky above. The Pokémon that dances in the heavens: Rayquaza. Rayquaza is venerated by the people of Hoenn as their protector and savior. When Primal Groudon and Primal Kyogre had battled for 20 dawns and 20 nights, the world began to lose its natural balance and tilt toward destruction. The people, unable to endure any more, cried out to their mighty savior Rayquaza before a great stone that shone with rainbow brilliance. And a change came upon Rayquaza, weaving in the sky above Primal Groudon and Primal Kyogre. Suffused in brilliant light, its body began to transform visibly. And then...
So yeah. Kyogre and Groudon get old and dumb (and strong) while Rayquaza gets powered up because of human faith or whatever.