Rayquaza has way more in common with a Chinese dragon than a cobra...
Anyways, the cobra is actually very, very, very possible and is what makes this information feasible to me (grain of salt still), though I should probably explain my theory, shouldn't I?
Reshiram could represent "good", as in what is pure and perfect. Ex. Garden of Eden, before Adam and Eve screwed up. Also, heaven.
Zekrom could represent what is already corrupted and dark, like death, violence, and other things. As in, the world outside of the sanctuary where you can actually feel pain and die. Also, hell.
The cobra could easily represent the temptation to ruin things, as in the devil or the temptation to screw everything up. The difference between temptation and corruption is that temptation means that it hasn't happened yet but could. In other words, it would represent Earth. You could go to heaven, but there's the temptation that can lead you to hell. Basically, it would represent the temptations and choices you face in life.
To put it simply, there's heaven, earth, and hell, each one represented by a legendary.
At least, if they did indeed chose a snake, that is most likely why. A snake can represent temptation, choice, and Earth. Perfect to complete the trio, I'll say. We'll have to wait and see if this is real, though.