I'd agree with you on the caloric intake. You can get fat from eating Broccoli and grilled organic skinless chicken breast if you ate 5000 calories worth of it, the same as if you ate 5000 calories of candy and fried cheese and burned less than the number of calories consumed.
However, nutritionally speaking I'd have to say that eating processed food full of preservatives, and artificial flavoring etc has got to be worse for your body than eating something that simply grew from ground.
I keep seeing these news stories that say "did you know that eating can help reduce the risk of ".
Humans evolved eating only stuff that came from the ground. The earth provides nutrition needed by a humans (not to mention every other species).
Not to say that processed food is devoid of nutrients, but there is no doubt that fruits, veggies, and grains balanced with a moderate quantity of meat is what the human body will thrive on.