I think what happened with Zygarde is that GF took some creative liberties and combined some of Jormungand's and Nidhoggr's traits. It's not like they haven't done it before.

As all but a few of us realize, pokemon are usually based on more than one thing. XY's legendary trio likely represents both figures from Norse mythology, and the XYZ axes. They also have a creation/destruction/preservation thing going on. For all of these to work simultaneously, GF had to give Nidhoggr some Jormungand traits.

Nidhoggr has no interest in preserving the world, he wants to eat Yggdrasil. So they took Jormungand's "holding the world together" thing and used it to make him the preserver.

If Yveltal is the Y-axis at the top of the tree, and Xerneas is the X-axis going around the middle, then at the bottom, Nidhoggr would just be part of the Y-axis as well. So they used Jormungand's "going around the Earth" thing to represent the Z-axis.

This is just theorymoning, after all, but I thought it made a lot of sense after looking at it this way, and I'm fine with it now.