UX design tools and processes are definitely lagging behind right now. The annotated wireframe document created in Visio, InDesign, OmniGraffle, etc. is still the norm. The closest thing we have to a solid prototyping tool is Axure (http://www.axure.com/), but creating anything beyond the equivalent of clickable JPGs is kludgy to say the least.
Kids fresh out of HCI and interaction design school are close to useless, because they have no experience having their designs developed. Seeing them interact with (frustrated) seasoned developers can be very painful. UX designers should learn enough about programming to be dangerous for many reasons, but hand coding prototypes probably isn't ever going to be a scalable answer. I fantasize about working on a next gen UX prototyping tool all the time, but, to use the article's metaphor, I don't have a dance partner for that.