I've researched the calories per sandwich, and a peanut butter and jelly sandwich contains approximately 318 calories while a ham and cheese sandwich only contains 241 calories. However, this does not include health benefits regarding sugars and proteins. Although ham is typically more difficult to digest, a ham and cheese sandwich proves to be a good source of protein while maintaining its benefit of being a low carb meal. Comparatively, peanut butter is a good source of protein and healthy fats while staying low in carbs; however, the jelly is the true downfall to the sandwich. Perhaps the best answer is to prepare moderate portions and alternate types each day depending what you are in the mood for. My personal taste preferences regard pb&j as a higher form of sustenance.
I agree with you. While jelly is the "downfall" of the sandwich, as you put it, I believe it's based on the type you use. My family grows their own strawberries and make the jam with little to no additives, thus making it healthier. However, there is also the factor of pesticides, but that can be delved into at a later time.
And yes, ham is a good source of protein and cheese is a source of calcium, but there's the factor of food allergies, such as one being lactose intolerant.