When we first implemented it, we went with a standard "First Person Shooter" coordinate system, meaning (for a person standing up, looking forward), X was the horizontal on the screen, Y was vertical on the screen, and Z was depth. Of course, if you change your perspective to now "look down" at the world (which is the standard way you start looking at stuff in Simio), those same axis now turn into X being horizontal, Y being depth, and Z being vertical.
We certainly could maybe rename and reorder them in the property grid or something to make more sense so maybe instead they maybe look like:
Vertical (old X)
Horizontal (old Z)
Height (old Y)
I don't know if that would be more or less confusing for users however.