Why rule out the possibility of the theme being genetics just because of this theory, rather than both themes being present in the games? I can't see much to the whole x-axis and y-axis thing rather than what Blade mentioned. It could be that part of the game took place in the sky, which I've got no idea how they'd make realistic to at least Pokemon standards, but I don't see a whole theme in it. But when talking these two legendaries, I can't see much to where genetics actually do fit in. The only thing that really springs to mind, is the rainbow-coloured light Xerneas sent out, which, as we've already talked about, could mean that Xerneas possessed all typings. It could be that Xerneas was genetically modified to be that way, or that some kind of cliche evil team would be out to get Xerneas' DNA to use it on other Pokemon to make them a lot stronger. That way though, I don't see how Yveltal would fit in, so it's most likely not that.