Hello there.
First of all, Mega Rayquaza is the best looking Mega Evolution I've seen so far, surely the nicest looking legendary with a Mega evo or the Primal Reversion duo. The Delta Stream ability makes it a bit of invincible though. I'll wait for the game to be released so that I can try it myself and see if that is the strongest mega Pokemon as well.
Regarding the story, the only logical assumption I have made is that Rayquaza was the first ever Pokemon to mega evolve. With Groudon and Kyogre gaining limitless power with their primal reversion and the threat to humanity and pokemanity, Rayquaza decided to mega evolve, thus gaining more power to protect the world from devastation (pun towards J&J intended). And since the secret of the mega evolution has been unveiled to trainers after the scientist's research, it has spread through most regions etc.
This theory has a strong disadvantage, reagarding the fact that trainers could mega evolve their pokemon even before the appearance of Rayquaza as the Messiah of Pokemon. Hence I can give two reasonable explanations, either gamefreak messed a bit up by forcing the appearance of mega evolutions in the Hoenn region (due to the remakes), or Rayquaza (and most legendaries therefore) knew the secret to mega evolution but didn't use it on will, and the special reason behind this evolution is the duel of the Primals. Anyway I don't wanna be boring, we will see it clearly when the game is released.
Another thing, regarding the remaining mega evos to be undisclosed, as many have stated we expect Flygon, Milotic and the latis, but I cannot stop hoping for a mega flying type. Like Staraptor or Pidgeot. Or this bad boy Luxray. Pokemon that can be obtained early in the game in general, the Nidopair or perhaps the Hitmon- chain. And also Pokemon with a two-lined evolutionary chain like Vulpix, Meowth, Psyduck, Mankey and generally the Pokemon that are considered weak. In my opinion this will make the game a bit more interesting, maybe difficult as well but surely interesting.
(Ofc I do not support that many Pokemon get a Mega, perhaps around 15-20 per generation, or the mega evolution will be nothing special eventually).
Concluding, I am a little bit disappointed by the megas revealed for Ωμέγα Ruby and Άλφα Sapphire (I'm Greek and the letters alpha, omega and delta are used in my alphabet, I feel a little proud for that). Salamence looks like a huge kite whereas metagross is now floating and got a huge sting on its face. Nothing special with Sharpedo's appearance as well, Camerupt is way too weak against water now and seriously, what would you use a mega Audino for, unless its new typing?
Thoughts? Can't wait till the final release (2 days before my birthday ^_^ )and what is coming up next!