Take heed that in the example above the subjects A and B may be dissimilar. You do not have to say how they were similar but only how they were noteworthy. It is also best to include three or more pairs when you are writing with the alternating point method because it gives your reader enough content to understand your subject matter.
Many professors prefer this method because it highlights the differences and similarities better. It also offers a more analytical and tightly integrated paper more often than not. If you can clearly identify the points between subjects A and B then this method of organization is best.