Microsoft has put in a lot of work to make Javascript a first-order language on par with C# for WinRT development. Both Javascript and C# have direct access to the WinRT API via language projections. That is, there is a unique binding specific to the language to the underlying API. So neither language is any more "native" than the other.
You should be able to write an equivalent Metro app in either language. At a high-level, it really does come down to which language/environment you are more comfortable with.
However, there are a couple of differences that should factor into the decision. First, WinRT components can only be written in C# or C++. Javascript can only consume thse components. If there is an intent to create reusable/shareable components, should keep this in mind.
Second, although the Windows Phone 8 SDK has not been released yet, there are indications that Windows Phone 8 apps can only be written in C#. If there is an intent to create similar apps for both the tablet as well as the phone, this is probably a serious consideration.
There haven't been a lot of performance-based studies comparing the two in a Metro app, so it's hard to say whether that will become a factor or not.
Then, there is also 3rd-party support to consider. C#/XAML is well established and has a lot of 3rd-party support. But similarly, Javascript has a lot of 3rd-party libraries available (e.g. jQuery) that for the most part can be brought in and used in a Metro app as well. I would give a slight edge to C#/XAML, but it seems like support is good for both.