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By RBY standards, MegaRay has 180 SpDef to tie with his 180 SpDef, he's 25% stronger and bulkier on the special side than mewtwo, letting him tank more than enough.
By actual gameplay standards, MegaRay has more than enough options to fuck up any form of Mewtwo (and before someone says "just icebeam lmao", Delta stream removes the quad damage) and while Mewtwo is naturally faster than Ray, MegaRay is capable of holding any item in his mega form, Mega mewtwos can't hold scarf, specs, band or life orb to become stronger or a sash to stay at 1 hp (which Ray can and proceed to finish the fight with ESpeed) which can just fuck up Mewtwo under any situation, MegaX? Dragon Ascent instagibs, MegaY? Good luck tanking an Espeed, especially if it was banded, Base form? LOL. And finally, seeing how MegaRayquaza actually created a tier above god's tier as the one and only banned pokemon from Ubers and has far more results than Mewtwo at VGC already puts Mewtwo at a disadvantage.
And by lore standards, Rayquaza on his base form is perfectly capable of telling 2 legendaries to fuck off while Mewtwo struggled to defeat its counterpart, Mew (inb4 hurr durr he was holding back) and also said 2 legendaries had Prime forms, which lore wise, also got told to fuck off by Rayquaza on his Mega form. And also said 2 legendaries are capable ot creating land and sea (respectively), what does Mewtwo do for the nature other than be a freakshow spawned by inhuman experiments?
