I find that if you're shooting from a tripod with careful rotation over the entrance pupil of the lens, manually specifying the control points is rarely necessary. The exception might be to delete "false" control points such as in moving clouds, waves, etc. Sometimes manually creating vertical or horizontal control points can also be useful to level the pano, but I rarely need to do so.
Autopano Pro is quick, easy, and relatively full-featured. For most images it will give results nearly identical to PTGui, or other panotools-based software. One thing I really like about Autopano Pro is that i has an uncanny ability to automatically set the correct centerpoint and level the pano, it will often do a better job of this than PTGui. The downside of Autopano Pro is that there's no support for manual control points, and it's missing a few features of PTGui Pro that I really like.
PTGui Pro is a very capable stitcher, with a lot of manual control. The interface is a bit clunky compared to Autopano Pro, but it has support for manual control points. It also has a projection mode called Vedutismo that I really like for wide to moderately wide landscape panos. Also, the support for exposure blending is very good. These last two features are the reason I tend to prefer PTGui to Autopano Pro, and if I had to pick just one stitcher it would be PTGui Pro.