Well, as far as Atkins is concerned, diet research is really, really hard and expensive to do right. I know because when I was an MIT student one of my jobs was office boy in the Food and Nutrition group, and I saw how hard it was. In one of the studies, research subjects were given a duffle bag from which all the input to their digest systems came, and into which all the output from the same went, for six bloody months.
Of course not every study needs to be that rigorous, but diet is one of those areas where the public needs lots of informed opinion but the funding for research is grossly inadequate to meet that need.
By the way, the current state of research seems to be that carbohydrate restricted diets work well in the short term but have only modest success in the long term.