Xerneas and Yveltal look very organic.
Xerneas represents a Neuron, Yveltal represents Muscles and Blood.
That means 2 of the 3 germ layers are covered.
Almost all animals develop out of 3 layers.
The third missing layer is the Endoderm.
The third legendary will represent the Endoderm.
This is some seriously deep and geeky theorising, which is nothing new to Pokémon games (remember that Ground Zero theory in Pokémon Black/White?). This latest theory also makes sense! Have a look at this image (click for full size):
All Higher Animals Developer Out of 3 Germ Layers [Turnip's Tumbles]