As a little background, I built the American Airlines Windows 8 app in HTML5. I have to say it was fantastic.
WinJs is not just some half thought webview implementation. Microsoft is finally showing JS the respect it deserves.
I would suggest getting up to speed with the latest and greatest in IE10. Honestly that is the core framework for all of the WinJs stuff. It is powerful and fast!
Also, here's a great place to get started with WinJs: http://msdn.microsoft.com/en-us/library/windows/apps/br211385.aspx
The future looks bright for JS as a native language for Windows.
Both. Because both are being adopted by developers (though not at the same time, what I mean is while some devs are using XAML/C#, some others are using HTML/JS). For those coming from a Web app dev background, it's easier to transition to HTML/JS. And for those aleady familiar with XAML through WPF and Silverlight, it would make sense to carry over the skills to XAML+C#. And as far as results are concerned, both technologies are showing good results. So my guess is both would be equally good in the years to come.
Metro Apps built using the HTML5/JS APIs will probably be classified as "simpler", compared to their C#/XAML counterparts. While the former will certainly be capable of creating functional, well designed apps, there will undoubtedly be a limit to the capabilities of an app built in HTML5. On the flip side, while C# might be more capable, it's also more complicated. An HTML5 app will be very easy to design and maintain, comparatively.
At least, that's my best estimated guess. I don't have experience developing Win8 apps (yet).
Both are going to run on WinRT (aka trimmed down version of Windows 8 which is used on MS Surface device).
It will totally depend on developers preference . Thus, developers with HTML5/JS experience will be equally powered to develop for Window 8.
For example, if you're running the Chrome browser, the V8 engine does just that which is mentioned above. It's my understanding that IE 10 is doing the same, as with the other prevalent browsers which support the ECMAScript 262 standard.
Not a MS programmer - From a programmers standpoint, it would be worth investing your time and effort in a platform agnostic, open standard like JS + HTML 5. The knowledge you gain can be re-used elsewhere.
Win 8 supports JS natively, so there wouldn't be much you cannot accomplish using it.