It seems like we're all in agreement: the web has changed, and smartphone apps and other methods of displaying and sharing information are taking away "market share" from simple web pages. Who's fault is it and what does it mean? That's more up for debate.
I agree with the authors that this change has certainly come and can be expected to continue to come. I don't know if hand-wringing is necessary. Anderson posits that it is the cycle of capitalism, but might it just be the cycle of everything? Everything waxes and wanes in popularity, and perhaps it is less a sign of corporate takeover of some of our freedom and more the natural development of the next form our communication will take.
Isn't app-to-app or object-to-object communication, though it may take place in a walled garden, a distillation of the point of the web? Information in one place affects the state of information elsewhere. If an app or internal network or walled suite of applications and things can do it more efficiently and enjoyably than even the most advanced HTML5 website, why shouldn't we just do that?
At the same time, the reframing of internet communications within private corporate settings is already showing how it can be a worse state of affairs. Telcos envision a more-walled system where Netflix and others can be paying partners rather than being neutral to all content. Twitter keeps closing doors to outside API users that the company had previously encouraged. Our willingness to accept the walling of the internet makes bad things like this tenable as well.