I was frustrated a bit by the dismissal of probability theory, though, as if Bayes theory solved it, and by extension, and probability as a whole could be dismissed.
A lot of the issues the author raises are limitations with Bayesian (at least classical Bayesian) theory. The author's critisms dovetail with some areas of probability theory (cf Jaynesian or algorithmic probability literature); I suspect their concerns are one in the same at some level as some of the concerns discussed there.
The problem is uncertainty to various degrees is fundamental to reasoning, so probability must be involved at some level. An integrated approach is needed. I agree that Bayesian theory per se isnt the end of the story, but something involving probability will be part of it (and because Bayesianism is a big part of that, probably that too).