Calories in / Calories out is still perfectly valid. It's just that the same portion of the same food might be considered a different number of "calories in" for different people.
The "big-boned" or "genetically fat" arguments still reek of BS, but it's worth humoring the idea that we aren't 100% efficient machines that absorb the exact number of calories on the Nutrition Facts box, or burn the exact number of calories displayed on the Treadmill screen...
There's a intelligent middle-ground between equally ridiculous ideas that we are "Healthy at Every Size" and that we are perfectly tuned biological machines.
That's the problem with the so-called "calories in/calories out" crowd: they think all food has a specific energy value that varies by statistically-insignificant amounts from person to person.
That people lose weight when they eat an energy deficiency and gain it when they eat an energy surplus is not in doubt. What some people refuse to do is evaluate whether the same foods have different energy values for different people, rather than one global value. I'm not saying they do, but the most ardent "calories in/calories out" fanatics refuse to even acknowledge the question.
I think human discipline is the most important factor in maintaining a healthy weight, and I find instances of "fatlogic" to be aggravating, but I'm not going to pretend that the human body is so simple that the Law of Conservation of Energy can be perfectly applied to our digestive systems...
Anyone who thinks the treadmill calorie numbers are correct is deluding themselves. As for calculating actual TDEE's, there are ways to do it (see https://www.reddit.com/r/leangains/comments/2rv09z/this_is_h...), and once you've determined your TDEE, calorie counting with something like MyFitnessPal makes it so you can know what you're really taking in.
They are convinced. And they will entertain no opposing ideas.