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Rayquaza is Quetzalcoatl.The Legendaries are pretty obviously intended to resemble the letters X and Y. This is to say that, beyond that I doubt they are designed after specific gods/legends/whatever.
Pretty sure it's based on this:http://en.wikipedia.org/wiki/Three-legged_crow
Just look at the name, the pronounciation is very similar to the coatl veltalcoatl
Also it's very 'modern', all about the mayan prophecy.
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