> WebGL and canvas are in no way replacements for the DOM.
That's kind of debatable. If you have access to a fast graphics layer from the browser, you can build a DOM replacement of sorts. I think that famo.us works kind of like that.
Core Animation is used by both the native GUI as well as the browser DOM. When you use layer-backed compositing on a web page (e.g. CSS 3D transforms), WebKit implements it with a Core Animation layer. So DOM-based rendering enjoys the same benefits of GPU-accelerated compositing as native apps -- although obviously with rather different semantics since HTML+CSS doesn't map directly to Core Animation.
If you implement your own GUI framework on top of WebGL or Canvas, you're not getting Core Animation compositing for free, so you need to replicate that functionality in your custom framework. (This applies equally to native apps: a WebGL app is equivalent to a Cocoa app that renders everything into a single OpenGL view, and a HTML Canvas app is equivalent to using a single CoreGraphics view.)
I don't think the WebGL/Canvas route makes sense for most apps other than games and highly visual 3D apps. You'll just spend a huge amount of time building your own implementations of all high-level functionality that is already provided by the OS and/or the browser: layer compositing, text layout, view autosizing, and so on. If you're doing standard GUIs, why go to all that trouble?
Not only that, but you can't make a 100% guarantee that your implementation will look and work exactly the same as the native one on the underlying OS. For instance, I can re-create all the native Windows UI controls and re-implement all their behavior in exactly the same way, but what if the user has a custom theme installed? Everything breaks. (WPF has a similar problem.)
Increasinly high end apps do.
The DOM definitely has its problems, mind you. Investing some time in designing a proper replacement for it is worth it, as long as people understand going in that the project might well fail.
The ones I've seen are actually faster -- Flipboard for one gets to 60fps scrolling on mobile, IIRC. And of course all WebGL based interfaces on native mobile apps that re-implement parts of Cocoa Touch et al, are not that shabby either.
Sure, it doesn't have as much accesibility, but that's something that can be fixed in the future (and of course people needing more accessibility can always use more conservative alternatives).
People have tried to replace things like text editing (with canvas-based editors), CSS layout of the DOM (with various JS solutions involving absolute positioning), native MathML support (MathJax; this one has of necessity done better than most, because of so many browsers not having native MathML support). There are a bunch of things out there that attempt to replace or augment the built-in form controls, with varying degrees of success.
https://github.com/domokit/mojo/tree/master/sky https://github.com/domokit/mojo/tree/master/sky/specs
None of the projects that you mention are really relevant to the discussion. I agree that they didn't change shit but it's precisely because they are still built on the DOM and cannot really go below that in the abstraction layer.
There exist UIs done in Canvas and WebGL that are arguably below the DOM in the "abstraction layer" and don't need to use much more DOM nodes besides opening a canvas/gl panel...
(Most full screen 2G/3G web games fall into this, for starters, and those are in the tens of thousands. But there are also lotsa apps).