I've suspected this for quite a while, and evidently, it's true. The claim that fruit and vegetables are inherently healthy is baseless:
In the best case scenario, an extra two portions of fruit and vegetables each day could prevent 2.6% of cancers in men and 2.3% of cases in women, the study concluded. [...] Fruit and vegetables could [...] be beneficial just by virtue of taking the place of more calorific fare, health experts say.
The following is the best article I've read so far on what we actually know about nutrition:

Science and Pseudoscience in Adult Nutrition Research and Practice

I stick to the following rules myself:
  • Calorie budget. I write down the number of calories in everything I eat. I do not allow myself to exceed my daily calorie budget. I pace myself throughout the day, eating 100-300 kCal every 1-3 hours, so that I can have a final meal of protein before I go to bed, without exceeding the budget.
  • Protein. I try to get at least 20g of protein every 3 hours. I get it from a variety of sources, including meat, yogurt, cottage cheese, fat free cheese, fat free milk, and protein powder.
  • Exercise. I go to the gym several times a week. Primarily weights, with cardio on some days.
  • Vitamins and minerals. I take one multivitamin pill each morning in an attempt to make sure that I get the vitamins and minerals I need. I choose a pill that has a 100% recommended daily dose for all the vitamins, and a variety of minerals as well.
I have found that exercise is definitely what makes the major difference, but keeping to a calorie budget and getting enough protein lets me keep my weight down and muscle mass up even when I get lazy about exercise for a while.