The thing is, Zone of the Enders was moving in that direction from the start. The first one was pure science fiction where Metatron is just a powersource. The second one moved towards fantasy with all that stuff that pops up about the Metatron. It's not really that strange.
Especially since traditionally Metatron refers to the angel that serves as the voice of God. I always thought it was weird that they named it that and didn't do anything with it.