Here are some articles discussing issues with Taubes' insulin hypothesis:

Stephan Guyenet, "The Carbohydrate Hypothesis of Obesity: a Critical Examination".
Lyle Mcdonald, "Insulin Levels and Fat Loss".
James Krieger, "Insulin…an Undeserved Bad Reputation".

The only way Taubes' theory would be correct is if there was a slowdown in metabolism when eating carbs, or an increase in metabolism when eating low carb, which would lead to a higher rate of fat loss.

To date there are no proper studies showing an advantage in or fat loss on keto when calories/protein/etc. is controlled, NuSI are doing some studies trying to establish what type of studies that are needed to support/refute Taubes' hypothesis. Taubes has some comments in a recent article on how far they've gotten, see "Chewing the Fat with Diet Journalist Gary Taubes" (thanks CharlieDarwin2).

I posted this in another thread:

If calories are held constant then you will lose the same amount of weight. There are lots of studies looking at this, here are some articles giving an overview of what they show so far:

Rani, "Disrobing Dogma – Low Carb And Ketogenic Diets In Weight Loss".
James Krieger, "Increasing Protein, or Decreasing Carbohydrate…Which Gives You a Metabolic Advantage?".
Examine.com, "What should I eat for weight loss?".

Some argue that low carb increase energy expenditure somehow, which would make low carb better as it allows your body to burn more energy with similar intakes (and possibly could explains how you'd lose more weight on keto).

Proactive rebuttal: The "300 kcal higher energy expenditure on keto!" Ludwig/Ebbeling paper has some problems, here's some criticism on that study, and there's some more recent discussion in this thread

So far there's no support in the scientific literature for the metabolic advantage idea; Taubes and Attia did a review of the available studies a while back and posted it on the NuSI site, see "Review of the literature" (click the "download summary of studies" red button on the left at the end of the article for more details). Taubes also discussed this subject in his Ancestral Health Symposium 2012 talk, "Calories Vs. Carbohydrates: Clearing up the Confusion over Competing Paradigms of Obesity" and explains what studies need to be done to prove/disprove it.

Perhaps their research with NuSI will show that there's a fat loss (metabolic) advantage, but until their studies are done there are no (well designed) studies showing that low carb would lead to more fat loss.