Puppet Master is great for the arms because they are sharply articulated at the shoulders and elbows and wrists. And if we developed the fingers on the hand, it would perfect for them as well. But some parts of the human body are a struggle with Puppet Master because they curve in soft ways. The human torso bends flexibly because of the many vertebrae in the spine. It doesn't make sense to cut this region up into little strips for Puppet Master sections.
Bones are a much better tool for the job.
The same is true for the hips. Bones are perfect in this area because, as the thigh lifts to step, there is a soft muscular pull all the way through the buttocks and the stomach. I've found it very difficult to divide this region of a character model up effectively for Puppet Master because there are no clear lines on which to carve up sections. Fortunately, you can use bones and Puppet Master together. Individual sections can have bones in them.