First we need to clarify your question; homogenization is simply the process of altering milk so that the fat will stay mixed instead of rising to the top when the milk is allowed to sit. Homogenization can be done to milk of any fat content: whole (3.25%), 2%, 1-1/2%, or 1%.
What you want to know is what is in whole milk that skim lacks, and the answer is, quite simply, fat. The only nutritional difference among the various kinds of cow's milk is fat content.
Infants and toddlers need a high fat diet; human breast milk is about 50% fat by weight; Fat contains more calories per gram than other foods (9 kilocalories/g, as opposed to 4 kcal/g for proteins and carbohydrates), so it is a high energy food. A baby has very high caloric needs relative to the volume of his or her stomach, so it's important to pack as many calories into each meal as possible to avoid malnutrition. For this reason, whole milk's fat content makes it more appropriate for small children.
Because of the high pace of brain development in the first three years of life, babies and toddlers also need a large amount of essential fatty acids, particularly linoleic acid, which is essential to proper brain and nerve development. Whole milk is a good source of linoleic acid.