The inertia and individual investment in HTML and JavaScript is so incredibly high that web players (from the browser makers such as Mozilla to the individual web developers) absolutely steadfastly refuse to evolve with changing requirements.
The belief that JS+HTML is "just fine" and no significant evolution is required to support application development is absolutely incomprehensible; what other application platform available today has seen iteration as glacially slow as the web? The browser makers have consistently stuck to their "HTML+JS is fine for everyone" guns, ECMAScript has failed to evolve almost entirely, and no common application development framework or platform has emerged.
HTML+JS libraries -- such as jquery -- are just fine for interactive document publishing, but are no replacement for Cocoa, Android, or Qt. The lack of common re-usable and extensible UI components is a travesty. Proponents like to advance the idea that this chaos is a benefit -- choose whatever tools you want -- but the rising popularity and the massive investment in application development on native app stores demonstrates a market desire for something simpler: A common well-defined application development platform is valuable, and the only barrier to adoption in the web world was a trustable distribution mechanism -- app stores.
The fact that you think App Stores will fade away is demonstrative of a failure to understand why the app store is so popular -- ease of distribution, easy to use common development platform, ease of payment processing, common UI (instant user familiarity), performance (!), open development platform (no JS sandbox, not all languages must be filtered through JS).
Ask yourself why Google has ChromeOS on one hand, Android on the other, and is working on technologies like NaCL that could bring many of the advantages of Android to Chrome?
Lastly, hopefully I can pre-empt the "JS is a common bytecode platform, just target that" crowd. Yes, you can emulate any other turing machine on top of a turing machine, but that doesn't mean it will be fast, clean, easy to use, easy to debug. It absolutely makes no sense to halt the evolution of the browser as a platform and instead tell everyone to use a high-level language like JavaScript as a common bytecode.
[Addendum]
I also should mention, anecdotally, that I've had some long-winded conversations with a member of the Chrome App Store team -- me from the perspective of a long-time native developer, them from the perspective of being tasked with coming up with ways to improve the web as an application development platform.
From my conversation, which may or may not reflect reality:
There seem to be two schools within the Google App Store team. The first (and seemingly most common) belief that there's nothing terminally broken with the DOM, HTML and JavaScript, they just need to find a way to make it easier to implement re-usable UI components, perhaps a common model for namespaces, objects, and other small improvements to JS.
The second seems to believe that a fundamental re-imagining is required -- perhaps dropping the DOM entirely in favor of rendering with canvas and a traditional view/event hierarchy. Consider opening the playing field for more languages (eg, via NaCL).
I think the competing strategies within Google and the clear differences of popularity between them -- Android, Chrome/ChromeOS/Chrome AppStore -- provide an enlightening view as to the likely future of application development on the internet.