I largely understand what he's saying, in terms of misuse of the protocol. I think you're going to find those sorts of things being the case for any toolset, though. Given enough time, and enough developers, you'll eventually run into people using it an entirely different way than you initially intended, regardless of the specifications or documentation written around it.

One thing I'm not sure I agree with, though, is the mobile application "linking" he mentions. When have non-web applications ever linked? What of all of the old "desktop applications" that everyone used to use? Those don't typically link, why is there a different expectation for mobile applications? Oh, and most mobile apps do support linking (in some sense, though it's not really a primary feature). Perhaps I'm misunderstanding what he means with this.