I believe there's some value and truth to conventional wisdom. For instance, I believe that the human body adheres to the first law of thermodynamics just like everything else, and that a change in energy flux inevitably leads to a change in body weight. Intervention studies support this theory - overeating leads to weight gain.
Calories are just as real as vitamins, gluten and phytic acid. It goes without saying that a proper diet plan should take into account the calorie intake, as well as the nutrient and anti-nutrient intake. The paleo diet is no exception.