Even so, the whole Mega-evolution thing is ill implemented and associating Rayquaza with it when Primal forms are available is bad.
That said, even if going with M-evolution, wasn't Lucario supposed to be the first Pokémon to have Mega-evolved? If so, since M-Rayquaza now Mega-evolves, it would make more sense (in my opinion) if Rayquaza were to be the first one to Mega-evolve (and retcon this bit). People already existed back then and so Pokémon and probably Lucario but wouldn't be better, storywise, to say that Rayquaza started it all and that Mega-evolution happens because when people needed the most (and I'm using the new revealed legend), they were able to link with Pokémon and so that bond is still present and needed for Mega-evolution? I always thought that Lucario being refered as the first one was kind of lamenot only because it's Lucario, a Pokémon that I'm sick of seeing, but also because it isn't a legendary, and since Diancie can Mega-evolve (I'm almost sure that idea goes back to XY and due to the games' lenght and number of Pokémon, I'm thinking GF already was way ahead with ASOR), why not give that honor to a legendary? Now that Rayquaza will also M-evolve and since its a Pokémon from ancient times, more sense it makes.