As a ketogenic dieter, Anahad O'Connor's article about ketogenic diets is pretty balanced, but his premise, described in the block quote below, doesn't hold up to much scrutiny:

Low-carbohydrate diets have fallen in and out of favor since before the days of Atkins. But now an even stricter version of low-carb eating called the ketogenic diet is gaining popular attention, igniting a fierce scientific debate about its potential risks and benefits.

I am grateful that ketogenic diets are being treated seriously enough to be written about in a national newspaper. Unfortunately, the New York Times is trying to teach the controversy, when no such controversy actually exists.

Here are some clarifying points about some of the topics discussed or touched upon in the article, from someone who actually follows a sensible, low calorie, vegetable-rich ketogenic diet:

1. There is no "Keto diet". There are a variety of ketogenic diets, all with the common element that they tend to put the body in a state of nutritional ketosis at some point (not all day long unless you fast; primarily while you are sleeping). All these diets involve restricting carbohydrate intake to very low levels, ranging from 0 g to about 50 g per day. They differ in meal composition, meal timing, and what foods are allowed or disallowed. Also, in real life, even people on ketogenic diets will eat a high-carbohydrate treat now and then.
2. Nutritional ketosis is not the same as ketoacidosis.
3. Ideally, ketogenic diets involve eating a great deal of high fiber (but low starch) vegetables. Imagine telling your doctor that you eat two huge salads per day, with four ounces of meat on them, one ounce of cheese, and a tablespoon or two of olive-oil-and-vinegar dressing. Doctors have told me that it is hard to eat healthier than that.
4. Ketogenic diets are"high fat", on a percentage basis, not necessarily on an absolute basis (as in, grams of fat per day).
5. Similarly, ketogenic diets are not necessarily higher in meat or dairy consumption that the standard American diet.
6. I have read many, many abstracts and articles about diet and nutrition studies. Almost every study I have come across demonstrates bias or lack of understanding of what ketogenic diets actually look like (they tend not to restrict carbohydrates in test subjects sufficiently), relies on bad data (epidemiological data, or prior studies' data, self-reported food logs), or have durations that are too short (you need more than a couple weeks to assess a diet change).
7. Sometimes the scientists' own conclusions do not seem to be drawn from from the data they collected. This often evidences itself when the study concludes that, despite outcomes being equal or better for ketogenic diets, there is concern about their heart health due to the amount of fat in their diet.
8. While you may believe there is insufficient evidence that ketogenic diets are healthy (whatever that means), there is ample evidence that the standard American diet (which I understand has spread to most of the world at this point) is obviously not. It it were, there wouldn't be an obesity epidemic.
9. I don't believe it makes sense to adopt an all-meat, or all-meat-and-cheese, diet. My reasoning: Fermentation of high-fiber vegetable matter in the gut is something humans evolved to do, and, for that reason, it is probably a good idea to continue doing so. I would understand if this argument were made more clearly in the article; instead some scientist’s statement that mistakes "high fiber" foods with high carbohydrate foods (i.e. starchy foods) is there, casting doubt about about the diet in a way that doesn’t make logical sense.
10. Ketogenic diets are not appropriate for some people, due to underlying medical conditions such as Type I Diabetes. This does not mean that that are not appropriate for anybody.
11. In the end, we are all n = 1 studies. It doesn't matter what the science says about a diet's effect on study participants or on populations, it matters how the diet affects you. Many, many people have success with ketogenic diets that they did not have with low-fat diets or with calorie counting. If low-fat dieting or calories-in-calories-out tracking works for someone, it makes no sense to disparage that person’s diet choices, and almost no one would. Ketogenic diets should be treated the same way.
    

All in all, the article is 80% of good content with 20% of nonsense thrown in for the sake of balance.