Good Calories, Bad Calories is often based on incomplete science. It certainly does not make sense when viewed through the lens of some of the largest human dietary studies ever performed (such as the China Study; which Taubes "debunked" in his own unique fashion, but he can't alter the fact that it's among the best, longest, widest, and broadest studies of human diet available; to ignore it is to ignore good science and put your faith in hunches, which Taubes has a lot of).
The Japanese diet is one of several high carb diets that leads to excellent health and longevity. Many of the most successful regional diets are based heavily on rice, legumes, and vegetables, and are very carb-heavy. Ignoring those historically successful diets requires either an extremely myopic view of diet, or someone who has a controversial new book to sell.
Don't get me wrong; I'm not suggesting that following Taubes advice would necessarily be a bad thing. He recommends whole foods, and cutting out sugar and simple carbs and processed foods, which are excellent dietary choices to make. Most Americans would get healthier by eating as Taubes recommends. But, to claim that a low-fat, high-carb, diet is unhealthy, when there are mountains of evidence to the contrary in the form of several Asian and Mediterranean diets, is misleading, at best. The problem with the American diet is not in any one macro-nutrient...fat or carb. It is that we, as a people, eat garbage at every meal. Processed, sugared, stripped of everything good and injected with everything bad. 80% of the food at a supermarket is probably something humans shouldn't be eating, even in moderation, but most of us eat it daily and as the primary source of calories.
Taubes is another fad diet promoter. His fad diet is better than most, and has some decent science behind it. But, it's not the ultimate reference, and it's not on my list of books to recommend to people who just want some ideas about how to eat better (I recommend In Defense of Food for that; it's anti-fad, free of hyperbole and outlandish claims and is based on tradition and science).