Why blend soup in blender if you can use a stick blender?
You've answered your own question in your comment, really.  One advantage of a stick blender is that you don't have to deal with hot soup in a stand-up blender. The advantage of a high-powered, stand-up blender is that it can puree very well.  However, hot liquids are problematic in these blenders. They expand and can create a mess, and potentially burn you if you are not careful and do not know how to control for this.  I use my stick blender for soups, but also for many small batch needs as well...when I don't want to drag out the blender, or the batch is too small for the jar.  So, in general, they are interchangeable, but in most cases the stand up version will puree more smoothly, and is (obviously) hands-free.