On the one hand, the number of calories you ingest is indeed an important indicator of obesity and its accompanying health problems. On the other hand, counting calories leaves no room for more nuanced understandings of what makes up those calories. For example, though the McDouble may have only 390 calories, about the same number of calories as an 8 ounce avocado, the ingredients of just the bun part of the burger are:
Enriched flour (bleached wheat flour, malted barley flour, niacin, reduced iron, thiamin mononitrate, riboflavin, folic acid, enzymes), water, high fructose corn syrup, sugar, yeast, soybean oil and/or partially hydrogenated soybean oil, contains 2% or less of the following: salt, calcium sulfate, calcium carbonate, wheat gluten, ammonium sulfate, ammonium chloride, dough conditioners (sodium stearoyl lactylate, datem, ascorbic acid, azodicarbonamide, mono- and diglycerides, ethoxylated monoglycerides, monocalcium phosphate, enzymes, guar gum, calcium peroxide, soy flour), calcium propionate and sodium propionate (preservatives), soy lecithin.
And we can only imagine how much longer the ingredients list would be once we factor in the meat, cheese, and condiments. So, although the single avocado may be considered equally healthy to the McDouble if we measure by calories only, there is clearly a large difference in the kinds of fats present, the amounts of preservatives with unknown effects, the other nutrients provided, not to mention the level of processing.
Despite the Men’s Health report, more people are beginning to realize that calorie counts mask other important nutritional information. This is perhaps most widely seen through the recent modifications to the Weight Watchers program. It used to only consider calories, such that a piece of fruit and a bag of low-calorie chips might have the same number of points (and each participant was limited to a certain number of points per day). Now, however, they’ve released a new Points Plus program, which tries to take other factors into account and now realizes that “not all calories are created equal,” with some calories being what they call “empty calories.” Now most fruits and vegetables are zero points, meaning you can eat far more of them. In the words of Weight Watchers founder “We are taking a stand for unprocessed food. We are taking a stand for fruits and vegetables.” Pretty cool.
Michael Pollan, as always, has lots more good things to say about the problem with nutritionism, or the ideology based on the “widely shared but unexamined assumption is that the key to understanding food is indeed the nutrient,” rather than the food as a whole or its context. Read more in his book, In Defense of Food, or in the shorter article on a similar topic, Unhappy Meals.
JH also asked,“What would be at the top of your list of healthy restaurants, and why would the chains mentioned in the article be at the bottom?”
In another comment, Mike addressed this question well, and shared the unfortunate fact that most national chains are by definition unhealthy, because of their commitment to uniformity, which leads them to “pump their food full of preservatives, processed food products, and CAFO meats.” Pretty much all chain restaurants end up serving highly-processed foods, because of shipping and manufacturing imperatives.
I suppose the chains that would seem the most healthy to me would be the ones that focus the most closely on whole foods and simple, mostly-unprocessed ingredients—this gives Chipotle a definite leg up, as well as Sweet Tomatoes and anywhere else with a salad bar that offers vegetables (though they will undoubtedly not be local and organic).
This, of course, just means that the best restaurants to go to if you’re thinking of your health are not any of the ones that Men’s Health would write about and instead are those more local and more interesting places that aren't constrained by national uniformity (as Megan indicates in her comment). But, yes, eating and cooking at home, where you can control what goes into your food, is most likely going to be the healthiest of all!