Hi Asher,
I know PTgui since 2003, but at this time there was no automatic control point generation built into PTgui. You had to choose two overlaping pictures of the project and had to visually and manually assign the control points. You had to be very patient and persistent. In later versions of PTgui you could run Alexandre Jenny's autopano standalone program or autopano plugin to create the control points...
http://autopano.kolor.com/
You always could manually reassign or correct control points by hand in PTgui. Autopano Pro did not exist at this time.
I first noticed Autopano Pro in 2006, but did not understand how it worked nor was I confident that it would do a good job. In 2006 I tested PTgui, PTmac, Realviz Stitcher and Autopano Pro with the Pinewood Panorama 1x12 captured jpeg files. PTgui was really good in automagically finding control points and in stitching. PTmac was only different in GUI and control point handling. Realviz Stitcher was so bad, that I didn't even want to find out how to improve the results. And Autopano Pro... I just didn' care about it as I was already satisfied with PTgui.
In May 2008 I tried Autopano Pro again (and bought a license), and really liked the idea, not to create any control points at all by hand.... but it took a long time for me to understand that you cannot even create pontol points by hand like I used to in PTgui. In APP all you do is to define an area in which APP may find control points by itself. Onthe other hand in PTgui you may assing only one control point, then another, or set the control point manually to another location.
But I am not a perfect user in both programs and have to learn more about APP. I think the concept of APP is hard to understand when you come from panotools or PTgui.
Karsten