Not sure if someone has already said this, but...
I think there should be more either built in subobject orientation detection tools, or easy tools to let the user determine the orientation of the subobjects. Like, you should be able to assign a normal vector to something by selecting a face with the same normal vector. And you should be able to select either a polygon or submodel to center the point on or in. The two might or might not have to be the same (if you select a polygon as the location).
Edit: and some easy way to flip points across planes parallel to but not identical to the three coordinate planes (i.e. the plane x = 2 instead of the yz plane, or any numerical entry); this would be particularly useful if you could do multiple points at a time.
Also, how about an "advanced clipboard" feature, where you can copy any number of points, subobjects, or what-have-you into the clipboard, and paste or remove them from the clipboard at any time. Also useful with this feature, you should be able to save clipboards, either inside their respective PMFs or as their own files.