I do wonder what Rayquaza's "connection" to Mega Evolution will be, and whether that's implying that Rayquaza will have a Mega Evolution rather than a Primal Form like Groudon and Kyogre. And speaking of Groudon and Kyogre's new forms, their new abilities are pretty awesome. Not only do they basically get their original abilities as they originally worked back, but now other weather moves can't cancel it out and then there's Groudon being unaffected by water moves while his ability is in effect, while Kyogre can't get hit by fire moves. I'd say this is especially neat for Groudon, considering that it's Ground/Fire in Primal Form, so it's biggest weakness basically can't do a thing to it.
Of course, this does make me wonder... What happens if Primal Groudon and Primal Kyogre fight each other?
Oh, and Groudon and Kyogre's new attacks are pretty neat too.
I still wonder how Groudon and Kyogre's new forms affect the plot and the plans of Team Magma/Aqua, although based on their new abilities, I think I can make sort of a guess.