The thing is that NaCl lets e.g. game developers use languages and tools _they_ like _today_ to generate great products that run with reasonable performance and are deployable to a decent app-store, here is a poster child: http://www.tested.com/tech/web/3263-how-bastion-can-run-in-a...
You can do the same with Emscripten + asm.js. You don't code in Javascript, you just compile to JS. The products will run with less performance than native, I'm sure, but at least they're not dependent on Google's app store.
And, for me personally if I'm going to run a native app, I see no reason at all to have it run inside a web browser.
