As to JavaScript, with WebAssembly coming, there may be options in the future.
Having developed many websites and many apps, HTML and CSS are really quite terrible when compared to something like iOS' auto-layout system, or even something like a DockPanel in Xaml (WPF on windows)
However, you wouldn't want to layout a document in Xaml or auto-layout either. Different strengths for different original purposes.
Personally I feel like a non-trivial part of why "web apps" (i.e websites pretending to be apps) generally suck comes down to this impedance mismatch
Those who do not learn the lessons from XML are doomed to repeat XML.
The DOM is simply an in-memory representation of an XML structure, and any attempts to populate a DOM with JSON (or YAML or ProtoBuffers or...) will simply re-create XML. CSS is a language for writing XML transformations (i.e. XSLT).
Of course, we already have JSON versions of schemas, transformations, xpath, namespaces, and incompatible decoders, so perhaps it is already too late for JSON.
With most "native" platforms you can have a WYSIWYG UI editing (because those markup languages were designed with that in mind). You visually define the layout (with mouse/trackpad), drop components there, and it's all nice and easy to use. Surely, you can code your UI as well, but to best of my knowledge no one in their sane mind does this, unless they have some very good reasons.
With web apps (progressive or not), the usual approach is to code stuff by hand, and see the results in the synchronized preview pane (or nearby browser window), patching the code until it all fits. Even if there's some tool/IDE somewhere that would let me bootstrap a React/React Native/Elm/whatever app with a mouse - by dropping a button on a pane and connecting an event listener with another mouse click (like I had it in Delphi, 15 years ago), I think it would be an exception, not a rule.
Or maybe I'm just unaware about how things are really done and have false beliefs, heh.
We could have a better DOM too. It could be more semantic, and more modular. The good thing is that on this one we are moving in the right direction.
CSS would gain by becoming Turing complete. It also could be aware of runtime values.
But yes, JSON, YAML, and ProtoBuffers are all worsened versions of it. The good news is that we abandoned SOAP, but at the cost of abandoning service directories too.