"Collections of div-soup activated by jQuery plugins are the way to write maintainable web applications that make sense"
It's not as though Javascript has no role whatsoever in custom elements, but really, there's a lot to be said about how this way of working will be a huge improvement over the current jQuery + div-soup status quo.
I'm saying that DOM through its relationship to HTML has weaknesses that make it unsuitable for building application components out of. "jQuery-enabled div-soup" is an example of how mixing presentation with model and logic yields unmaintainable results.
I have been interested in React.js recently, since it provides an interface to create reusable components and to use them inside a rich programming language with full types. I think that's a better example of a competing idea.
My experience is with building single page apps from scratch, so maybe there's a common use-case (embedding a twitter widget, or a 3rd party comment system in a blog) that Shadow DOM and Custom Components will address that I'm not familiar with.
One is better encapsulation, another is a well defined styling system (although obviously this article shows that this is not a super simple problem to solve, I'm certain that a good way of doing this will be around before too long) --- finally, and the most important thing, is that it's just baked into the platform itself, so interop between different frameworks is less of a pain.
For instance, suppose you want to use a particular Ember component in your Angular app. You probably don't want to include the entire Ember environment, and you want it to play nicely with Angular's idea of data binding and local scopes. Can you even do this? If you can, how much effort does it take, and how much does it degrade the application?
So, we've got: interoperable components/widgets. Easily style-able widgets. Elements with some semantic purpose. Simplified documents. Reusable templates (which, once HTML imports are pref'd on by default, should be easily host-able on CDN hosts).
There are a lot of benefits to baking this into the platform, despite making the platform an even bigger, crazier mess than it already is. It should hopefully give us better (and better designed) tools to work with.
Granted, I'm not saying it's going to solve every (web) problem ever, nothing ever does.