The right question is: "are there any substantial apps that take advantage of native Web Components (polyfill or not)?" The answer to that is: "yes, a lot."
Polymer is just one way to write the components. X-Tag is another. Pure JavaScript is another. Use one of them or use them all. No big overarching framework required.
But it's not just about writing individual components when you build an app (you need something like a router still for instance). I say this as someone who rather likes the model Web Components espouses. Developer ecosystems matter a lot - for development, debugging and hiring. At present you have a great many more resources/communities to reach out if you go with React. When you get stuck with Web Components or polymer, and you will get stuck, you are a lot more on your own.
Also, for building you are, at least presently afaik, limited to vulcanize instead of the richer set of tools out there for more typical patterns. Vulcanize is cool, but again - if you get stuck, and you will if you do something complex - you have to rely on a much smaller community to help you out.
