The elephant in the room is sweat chloride, which was an original study endpoint. Had they been able to give a logical explanation for the lack of reduction in sweat chloride AND shown the FEV improvement they have shown then the skeptics would be converted.
Biology doesn't always follow the timeline of an experimental hypothesis. Anecdotal reports by patients with non G551 gating mutations receiving Kalyedco are demonstrating early improvements in FEV-1 just like in this study, with sweat chloride slowing improving subsequently over the first three months of treatment. The theory that sweat chlorides have to be linearly improving at the same pace (or sooner) than improvements in pulmonary function were not correct assumptions as evident in homozygous 508 CF patients, as well as the non-551 gating patients reporting pulmonary function and subjective symptoms improvement before seeing sweat chlorides dropping so far. The most important point is that the results are statistically significant in the treatment group using 809 with Kalydeco and that FEV-1 and not sweat chloride, is the end point that the FDA will use to judge the efficacy of these drugs.