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.
...the Pokemon creators likely chose Rayquaza to get a mega evolution instead of a primal form to set it apart and above the two mascot legendaries of the Hoenn remakes.
They may have done it to set it apart from Groudon and Kyogre. For lore reasons, refer to the first quote. Alternatively, they may have just wanted a stupidly overpowered Pokemon that people could use. Ultimately, only Game Freak knows, but speculation can be had nonetheless.
Hope I helped!