I'm going to go ahead and guess that the people behind Qubes were worrying less about the fact that the desktop paradigm may be fundamentally flawed in terms of usability (not going to argue on that one), but more about security, which is the stated goal of the project. Desktops may be on the way out, but that doesn't mean that we can't do some very basic security work on the heart of the OS. Looking at some of the documentation, it appears that their VM-per-application-group idea could scale very well to touch- and app-based interfaces with some work.
Security has a vital place in every OS, regardless of the skin you put over the top of it.