It is unfair to judge the essay on the basis of the current OneNote UI (e.g. its lack of alphabetization unless you Bing later addons), but it does seem to gloss over controlled user experimentation, and the importance of design patterns recognized by users — even when developers hold their noses to legacy approaches. The decline of extensive user-settable preferences and a NIH tendency to create options that are cool and unique vs. readily grasped standards may reflect some unhealthy temptations. A similarly curious journey can be found in the history of tags and folders in Gmail.
We are undergoing a dumbing-down of UI now to support mobile even though Hi res desktop monitors ought to be ushering in a better high-productivity workstation experience.
What is cool, as with what is efficient, or handles exceptions smoothly, is highly task-dependent. And often a somewhat pedantic undertaking for designers.