I'm importing AC3D models into Targetware, which has Z as the up/down axis, where as AC3D has Y as that axis (or it's reversed... but you get my point).
Because there are a lot of files with specific x,y,z locations, and directions for rotation and movement of objects, you have to make a lot of fine alignments, etc. for things to animate properly. Reorienting a model while trying to import it into Targetware can be a nightmare: you're trying to move an object .005m in any given direction, and the orientation differences make a positive value a negative, or changes the order in which you order a ##,##,## line of values. In short it's a major headache and adds several x the hours needed to perform these tasks.
I've also noticed that 3DMax, and I also think Lightwave, Maya all use "Z = up/down" orientation, and AC3D is the "odd man out". I don't necessarily feel you
have to conform to this convention, but being different does have repercussions.
I'm dutifully trying to figure out ways to "not make it an issue", and the idea of solving the rotation problem from the get go would be fine, if only I could have my viewports showing me "Top" when I'm looking at the top of an aircraft, and not the nose.... and in the other case, if it still feels intuitive to spin around a model as you work on it and inspect it in 3D view, then I can very easily just model my objects "on their sides" in the future.