There's value in enumerating important principles for consistently pursuing quality work product. That's why the Agile Manifesto has value. The manifesto is just a manifesto, a statement of intent and principle, and not a methodology in and of itself. One doesn't need a published, monetized methodology to engage in agile software development. One simply needs a methodology -- whether unique to one's project, or widely known -- that reinforces those principles to engage in agile software development.
The biggest problem with agile software development as a concept is that it, like any other elaboration of any principles of quality work, is that most people will fail to see the forest for the trees, will marry themselves to some well-marketed thing that pretends to be about principles, and will end up largely doing the same dumb crap they've always done.
Sometimes just documenting what the thing is supposed to do and why would solve so many issues, but since people have gotten hooked on capital-A Agile so much has gone by the wayside, or been delegated to non-technical roles.
-value trust over plotting and scheming
-value open communication over hoarding information and deception
-value disarmament over preparing for battle
While we value the things on the left, we value not getting steamrolled by people who practice the things on the right even more.
No, that's not the problem with the five values and twelve principles.
In fact, the problem is the desire to have a single, divinely ordained methodology (which both the first value and twelfth principle reject, and that rejection is arguably the central basis of Agile.)
OTOH, while it is good that the Manifesto and Principles don't ordain a methodology a it's bad that they are written in a way which makes it harder to extract actionable direction than is necessary.
Most of the problem described in the article -and everywhere- is precisely that "the theory is good but everybody is doing it wrong".
But that doesn't really help, because it overlooks the fact that the origin of all this is just a pile of generic, hard-to-argue small-time guru ruminations. I mean, it is not necessarily bad advice: "These are valuable things and we think that in particular these ones are more valuable than those other ones". Okay. Probably. They do look good. Let's say they are. Now what? Oh, that's left as an exercise to the reader.
It's funny. Just yesterday I almost had an argument over one of these things. I heard Karen say to the guy on my left that "Agile means less documentation", so I raised my eyebrow. "Agile means less defined documentation, more open, because documentation has no value at all" - she added. I was about to point out that that is not at all what it means, but then she went further and told him that what he needed to do was to "work as a team and become more involved in collaboration". That, right there, is the problem: pretending a bunch of cool sounding expressions can be a substitute for actual things like writing down what they wanted the guy to do.