The core issue, I think, is that software development remains unpredictable in many very common situations (for a whole lot of reasons, most of which are not technical). Management and planning requires predictability, so we devise systems like Agile to attempt to impose predictability. This addresses the wrong problem: the work itself is unpredictable, no matter how predictably your sprints start and end and how well you fit X% of a project into each sprint. Things improve (in many cases thanks to systems like Agile) until they hit a local maximum constrained by that fundamental unpredictability, at which point planners and management are still unhappy, so more process is imposed, abd eventually we end up in the situation described by this article.

Usually,causes of the fundamental unpredictability remain unacknowledged and unaddressed beyond a superficial level.