This is a great question.
Taubes framed his conclusion as an overall reaction to his immersion in the research. He also frequently notes his tendency to prefer the insights of clinicians, who actually have to treat obese patients, to those of researchers, who often lack direct personal experience with obesity or treating obese patients. So, in a sense, Taubes is speaking with regard to individuals who already have broken metabolic and hormonal function. And these individuals tend to tolerate carbohydrate poorly.
Guyenet - unlike Taubes - admits that he has always been slim and never really had to struggle with encroaching weight gains. So it is a little easier for someone like Guyenet to view the matter from a pure food reward perspective, which implies that removing one source of reward - be it fat or carbohydrate - will have similar effects.
We Paleohackers know - quite intimately - that a low carb diet rich in fat and protein can be very satisfying and enjoyable, once our fat burning pathways have been established. The literature suggests that low fat or calorie restricted diets, on the other hand, are very unsatisfying and unpleasant, and thus represent a less desirable strategy for treating obesity, even if in some strict sense Guyenet's food reward theory is correct.
One problem with both theories is that they are too simplistic and reductive to work as complete or overarching theories of what causes obesity or of what caused the obesity epidemic. That said, we have at least one reason to privilege Taubes here, because the obesity epidemic did not co-occur with a sustained increase in fat consumption, whereas it did co-occur with a sustained increase in carbohydrate consumption. Then again, in Guyenet's defense, there is co-occurrence with low quality forms of both macronutrients: processed carbs like HFCS and white flower, and industrial seed oils.
Taubes' notion that insulin is a fat storage hormone is pretty well established, but he frequently noted that researchers had that part figured out in the 1950s (if I recall correctly), and I don't know where the current literature stands on this. Taubes definitely placed an undue emphasis on insulin, however, as leptin is probably just as important. Since the same dietary protocol controls both, though, this shouldn't matter too much.
I think the basic idea is that - as mentioned by Cliff - chronically elevated insulin is the issue. And processed carbs certainly contribute to this state. When insulin levels are chronically high, we become less able to handle it, which is what insulin insensitivity is. I'd be surprised if Guyenet disagrees with this.
My conclusion from all of this is that for those who are like Guyenet and have healthy metabolisms, fat and carbohydrates can be thought of as equivalent sources of food reward. But for those of us like Taubes (and me) who have struggled with weight gain, and thus probably have broken metabolisms to some extent, we have to pay closer attention to our carbohydrate intake. We cannot deal with the insulin spike properly, which - skipping over a lot of biochemistry - is in part what leads to chronically elevated insulin levels in the first place, as well as the fat storage patterns that Taubes makes central to his explanation.