I assume you are talking about cow's milk in your question. The only difference between whole milk and skim milk is the amount of fat that is present. Since fat has 9 calories per gram, as opposed to 4 for carbohydrates and proteins, the reduction in fat content means that skim milk has many fewer calories per serving than whole milk.
The average adult gets plenty of fat in their diet, and most adults should switch to skim milk in order to get the calcium benefits of dairy without adding excess calories or fat to their daily intake. However a two year old has a very high metabolism due to growth and activity levels, and a very small stomach. Most nutritionists advise not trying to feed toddlers a low fat diet, because doing so creates a real risk of marasmus, a nutrition deficiency disease caused by lack of caloric intake. At Tim's age he is undergoing a lot of brain development, and he needs fat and calories to support it.