Is it possible that, instead of Melia or Erin, Madame X could be Alice? Or at least, a version of her. It fits with the "Father, I have failed you" aspect, she's been shown to not be entirely trustworthy (at least she has been in V13, but I doubt what happened at the pyramid will happen again here) and she has an affinity with dark types, of which Yveltal is a part of