Is there an article or something where they told us why they made Mega Rayquaza even more powerful than Arceus, the god Pokemon? I mean it doesn't make much sense.
Mega Rayquaza was a Pokemon meant to serve as an 'epic conclusion' to the tale of Omega Ruby and Alpha Sapphire. This is one possible reason.
But really, we can't tell. Only Game Freak can truly answer your question.
In Pokemon lore rayquaza was given a mega evolution by Arceus to make it stronger in case groudon and kyogre started fighting again. As Arceus knew that kyogre and groudon would be more powerful also. Mega Rayquaza was meant to be able to fight and defeat Primal groudon and primal kyogre at the same time so he had to be strong