After alot of mulling it over I'm having to settle with team Sci-fi on this one 
[feel free to skip the next bit as it is a little waffley}
I figured that for the sake of this battle between the forces of fantasy and the forces of sci-fi, all the humans would reside on the sci-fi side (essentially an augmented reality) whilst all the magical and mythological would reside within the fantasy side.
For these two forces to actually fight each other they would have to exist within the same universe so each side is not necessarily restricted to their own technologies.
I've always seen the real human strength as being the adaptability to survive, in this case with the advances in science and technology:
Gaia is the god of creation; G.A.I.A is advanced technology that harnesses and manipulates it's power. So whilst the fantasy armies amass and pray to their god for her blessing, team sci-fi barges in and greedily takes it all.
For the battle G.A.I.A's power is insurmountable making her and her pilot the ultimate grand supreme hero of the ART WAR.
I cannot however envisage tea sci-fi lasting for too long on it's own as power struggles will bring about self consuming wars that end all humanity.
(also hopefully I'll come up with a suitable acronym for G.A.I.A as at the moment the full stops are really just to make the name look more sci-fi)
Design wise, I want to mix in visual aspects from a large variety of religions, the bursting organic qualities of nature but most importantly the sci-fi elements; the attempts to restrict and control the force of nature.
Anyway, here are some thumbnails and sketches 
