Probably square yeah, it seems very hard to implement hex grid on 3d. Age of decadence was suppose to be hex but they had to switch to square because it was too hard to do in 3d.
But I really don't see why a turn based game should have to use 3d, 2d is obviously better. Gamplay matters more than graphics... that's what made fallout 2 great, gameplay...
I prefer hex, more natural and intuitive.