I think during previsualization and early development both Legendaries had alternative formes that tied into the story. Yveltal would have had a "Cacoon" or "Egg" forms where he was tucked tight in an ovoid shape. He may have entered battle in this forme, and like Regigigas had an ability that hampered his damage; the secondary forme had incredibly high defense and special defense to compensate. As he was attacked, the act of violence against him would trigger his forme change; as an allegory to mankind destroying the environment, and warfare.
Xerneas would appear in the story first as a tree, in a suspended state. It was to function as a guardian to those who would seek out Yveltal; as well as their own destruction, which would be ushered by this action. The Neutral forme was also going to be a similar state to Yveltal's alternative with boosted defensive stats, but as Xerneas attacked more it's stats would change; as a symbol of it's own reluctant acts of violence changing it's nature.
