In terms of lore (not game mechanics how would the legendaries be ranked? I always figured it was something like this.

Arceus (god of all creation)

Creation Trio (gods of the cosmos can never be destroyed as long as the universe exists)

Xerneas and Yveltal (demi-gods of life and death, as long as life and death are abound they will never cease to exist and can never be fully "destroyed")

Rayquaza/Groudon/Kyogre (ageless yet mortal beings, incredibly powerful yet not gods/demi-gods even with their primal and Mega forms).

At least that's how I see it