Great news! It appears as though a snippet of the plot synopsis has leaked online somewhere and sheds some light on what you guys have been talking about: the villains. I am spoiler-tagging this because some of you may not want to read it yet:
"Cia, having been brainwashed into attacking Link and Zelda, falls after a long fight with the group. She then realizes her mistake in combatting them, immediately after the corruption was vanquished by the enlightened power of the heroes.
It is then that Wizzro, the bewitched ring-turned-sorcerer, arrives in the form of a black cloud-like mass, apparently having survived his previous encounter with the heroes. As it turns out, he was using Cia the entire time, seemingly under her leadership; he slowly siphoned her power without her knowing. He then saps what is remaining of her power and turns into a dark beast."
So it looks like some of you were right. Cia is a mere puppet which was subjected to Wizzro's power to steal the power from his hosts/owners
Unfortunately though, this seems to be the only new part of the synopsis as of now. Whether or not Ganondorf is behind it all is still unknown