My printer has a fan that blows that happen to appear on the side for most models from thingiverse. Rotating those models so the front faces the direction of the fan helps in most cases. But I keep forgetting to do this. If the Preferences -> Models have a default transformation that can be specified and applied for every object when it's added that would be good. Of course, there should be transformation for the individual object on top of that just like it exists today.
This feature has been added in version 3.0. Just go to Tools > Options (or Simplify3D > Preferences on the Mac), click the Models tab, and setup whatever Import Actions you need. For example, rotate every part you import around the X-axis by 90 degrees.