Still, I take the point, but it still seems to me much more like something that would be theoretically possible than anything that will actually come to pass. As you say, to really make this happen, you have to stop limiting the progress of HTML, and that means breaking out of the browsers.
But ... if you break out of the browsers, you fracture the platform, and that means you lose the incentive to make these apps web apps in the first place. If your HTML/JS/CSS stack isn't as platform and browser-agnostic as it can be, ultimately you end up with a platform-specific way of writing apps that competes with native apps, and that's a losing battle.
Putting that aside, I'm not sure there's case that all apps should be HTML/JS, either. We can do cool things with the web stack, but ultimately it's designed and optimised for sending pages and forms back and forth. We put up with that because there are a great many benefits in doing so, but there has to be a reason to write our apps that way -- reasons that things like iTunes and the Safari Web Inspector have, but lots of other desktop apps don't and won't.