Hi Stiglr,
I'm not sure that AC3D is the 'odd one out'.
Lightwave has Y axis up/down, Z axis in/out. Other programs that I have tried and conform to this description include:
Poser, Lifeforms, Daz Studio, Bryce, Wings3D, Deligne3D, Polytrans
The only 3d objects I have ever used that gave me problems were .3ds objects.
Now maybe these programs have some kind of 'Preference' setting that will allow a re-orientation of the axis .... maybe we can get feedback from people using other programs.
Regards,
griff