That being said, this is an awesome Tool!
I know projects like GWT or LibGDX would benefit greatly from something like this, and personally while I like coding JS, I prefer my prototypes to be in JS and my final code to be in Java. (I know, heresy).
You are doing amazing work btw.
Surely we must know better in 2013.
Having said that, it also has a lot of cool features and I use it every day. Most of the time, I find it a decent enough experience.
Like it or not these developments are turning JS into a bytecode for the web. Maybe one day there will be other language options but why not invest in making the best of what we do have?
No, we should grab the first thing available and run with it, making sporadic additions and optimizations to do cool-thing-of-he-day, completely ignoring overall architecture and neglecting original purpose behind the technology we use. Next stop: compiler that will translate C code into Excel macros.
However, for people who want to have an edge, as developers, working in their language of choice is one sure way to get it.
There are many different developments to make that happen, like languages that compile to JavaScript, or binaries that run in the browser via NaCL; I think there's a lot of potential there.
... JavaScript was not a language designed with software engineering in mind; that much should be clear. If you can choose the proper language for the task at hand, instead of simply being forced into JS, you'll be ahead.