Having already built an application using TVML/JS and now working on a native application I would say that the Javascript option is aimed more towards beginners or basic applications.
TVML applications provide an easier, faster way to build standard applications with common features/user interface. We used it to rapidly build a prototype of an application. Now that we've launched the application and it's getting some uplift (featured in What to Watch and Top Free Apps UK) we are now rebuilding it natively to add additional features such as analytics, crash reporting, custom interfaces and other bits to increase re-circulation and custom recommendations.
@shirefriendship's answer provides a good explanation to the benefits of TVML applications and I think this is a good option for beginners, prototype applications or even basic applications.
Native applications provide alot more control over how the application looks, works and feels. Having access to most of the iOS SDK's allows you to do more such as integrating Cloudkit, develop 2D & 3D games and more.
Once we have finished development of our native TV application I'll update the answer with some more information such as development time between the two different versions, features in the application etc.
UPDATE: To answer your second question, yes you can pretty much develop ANY user interface / template using UIKit, the TVML templates provide user interfaces that would be commonly used / quite handy. Using UIKit you could replicate or customize any of the pre-defined templates or build something completely new.