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).