I dont have a problem with this article, personally I think the results are rather interesting. Does the study have flaws, potentially, can you draw any general conclusions re BF vs Shod, not really. But unless you believe that they faked the results, then the results can be used to draw some conclusions. You dont have to agree with their conclusions... but that is a fundamental aspect of science. Conclusions are not meant to be agreed with.
Personally i know that my performance will allways be better in a pair of shoes, simply because no matter how much i try i cannot throw all caution to the wind and go hell for leather BF, i can if i have racing flats on.
I do note its constrained to hard surfaces, i prefer to run BF on soft natural surfaces, It would be interesting to have seen the efficiency if Kram had followed his hunch another step and had the runners run shod on the padded surface. the results of which may have then been of interest to competitive cross country runners.
Besides if the Majority of us are into BF running for other reasons than pure performance then the results of this study have little bearing on us at all. Just as I imagine a study looking into the subjective enjoyment of running would be of little direct use to those primarily interested in performance.