Of course calories in/calories out explains your weight loss/gain. I haven't seen a single study that shows anything except this.
But of course that isn't the whole story.
The big issue with using calorie restriction for weight loss is that it take significant self control for long periods of time (months).
People take that as a moral judgement of people who don't lose weight: they assume that it means they are mentally weak.
But the truth is that there are alternatives. The thing that most calorie in/out advocates miss is that it's calories over time that matter. If one can spread digestion of the same calories over a longer period of time the subject will generally feel less hungry.
This is where high-protein, anti-processed food, anti-sugar and insulin reaction people have a point: High protein, high fiber and unprocessed foods generally have a high satiety index[1][2]. This means a person eating them will feel less hungry for longer for the same amount of calories.
Naturally this links back to calories in: if someone who is trying to lose weight doesn't feel hungry they don't have to have so much self control.
To me the low satiety index of confectioneries and soda drinks explains why sugar is so dangerous: It's digested very quickly and contains lots of calories, which is the worst possible combination for weight control.
I don't understand why satiety isn't discussed more in weight control, since to me it is the key factor.
(This is all from the perspective of someone who lost nearly 20kg via calorie counting)
[1] http://www.ncbi.nlm.nih.gov/pubmed/7498104
[2] http://www.ernaehrungsdenkwerkstatt.de/fileadmin/user_upload...