My guess is because Nintendo has this mistaken impression that Rarity = Power, considering back in the day Mew was a big deal because of its movepool and Power Creep hadn't caught it yet.
That said, the entire point of the story is to say Rayquaza can beat Deoxys, ergo it's weaker than the Rayquaza you're letting into VGC.
I don't get exactly what they hope to accomplish here though. I accepted Mega Rayquaza in some degree because Rayquaza was already Tourney banned, so it was creating this awesome Mon that was basically bragging rights reward for finishing all the "story" content, so there was no danger in making this ridiculously over the top OP Mega form. Now that it's being let into VGC, they are bringing into (what should be) a balance based Game space an element that was explicitly designed without balance as a restraint.
It's not even like this is a first mistake: They acknowledged that Mega Kangaskhan was ridiculously dominant in VGC, and there's also the matter of all those other strats like Intimidate Spam that cannot be ignored. They know that if they add an option that is very low maintinence/risk and high-reward, every player is going to use it. And unlike Kangaskhan, even casual players have to realize Rayquaza is nuts considering even as legendaries go, the entire Delta Episode was about hyping its Mega up.
I also wonder if they realize they're now going to basically turn a lot of VGC teams into those Battle Spot ones where people throw 6 Uber Mons with little rhyme or reason.
