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Ever since Generation III, Rayquaza seemed a bit weaker than Deoxys due to the fact that Deoxys has 4 forms, and its Attack Form has a whopping 180 Attack stat and Special Attack stat. Now Mega Rayquaza has the same Attack and Special Attack stats as Deoxys. At the same time, Groudon and Kyogre both got new Primal forms. Mega Rayquaza also may have been made to get himself a new form. This is where the question starts. Was Mega Rayquaza made to catch up with Deoxys, or to get a new form like the rest of the weather trio, or both?

Mega Rayquaza was created in order to out-swag every Legendary Pokémon ever and every Mega Evolution in the past, present and future.

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Mostly to get a new form

Here's why:

a) Legendaries aren't meant to 'catch up' with other legendaries; they form an integral part of the story, and therefore don't go around comparing powers

b) Rayquaza was never 'weaker' than Deoxys. Not now, not ever. With those defences that give competition to a wet toilet paper, Deoxys (Normal, Attack or Speed) can't win against Rayquaza without a Focus item. [Extremespeed FTW]

c) The new found power of both Groudon and Kyogre causes great imbalance to everything. In-game, meta-game, everything. So, to keep them in check, Lord Rayquaza descends down to save us all (mostly because Arceus is lazy and prefers sleeping for eternities instead >.> )

d) Everyone else was getting a cool new form too

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thanks for ba :)
Your welcome.
This answer has been in my head for a long time but I know that this answer is incorrect because in the movie, Destiny Deoxys, Deoxys had two opportunities to defeat Rayquaza. In the first battle, its vision was blocked by electro magnetic fields, and in the second battle, it was interrupted by the other Deoxys. So regular Rayquaza doesn't stand a chance against Deoxys, but mega Rayquaza does. Even then, in pokemon generations episode nine the trainer caught Deoxys and there wasn't a full-out brawl like the movie, but the episode is a direct reference to Pokémon Omega Ruby and Alpha Sapphire when you go to fight Deoxys in space, in which Deoxys was level 80 and could one-shot Rayquaza with its best attack (I forgot the name of the move). But it just shows how powerful Deoxys is and proves it is even stronger than Rayquaza.
I looked more into mega Rayquaza and found out that it is indeed stronger than Deoxys, way stronger, but regular Rayquaza is still weaker than Deoxys sadly :(