I mean, sure Kyurem is rumored to have eaten a good percent if the population in that one well walked town, but the player really doesn't face it when it was naturally evil. And then there's Darkrai, but that was just only available as an event side quest.
So, would a legendary Pokemon that's bad from the beginning and after the end work for the main plot?
Or is Gamefreak going to stick with Humans bring the source that makes Pokemon do bad things?(Ie, all the negative actions by the Pokemon to humans generally root back to the humans provoking it through negative means.)
"Good" and "evil" are childish distinctions with no real application in the real world. Pokemon is pretty much the only franchise aimed to children that at least tries to be morally grey (even the "villanous" teams have some sort of reedimg quality and aren't inherently evil), like everything should be. It should stay that way.