While 1) is true, it's not significantly true. If we are measuring calories consistently, even if we are wrong about it, we can continue to trend downwards until we are losing weight. There isn't such a massive difference that caloric measurement error is to blame.

And for 2) this is really not true at all. Yes, you might store fat temporarily etc., but if you are eating a caloric balance, guess what: that fat has to be used at some point.

Taubes is not wrong, but he really overemphasizes a lot of things. People who are obese are not eating just a little over caloric balance but eating the wrong things. They are eating massively over caloric balance. Cutting sugar out might be a good way to get them to comply to a diet that requires them to eat fewer calories, but ultimately for the obese it's really just the calories that are an issue. Imo this warrants more research into the psychological aspects of obesity (the food dopamine reward system etc.)