Javascript is also supported as a language to develop native apps by communicating with WinRT, the new runtime.
I know, but Microsoft needs more developers on the mobile side, which is laking of applications, than on the desktop side.
sure it does, so what is your point? Native apps still rule mobile, so MS makes a smart move by allowing javascript in native apps. This way they lower the barrier for web developers to start with native development.
And yes I would also at the same time try to get more love on mobile web sites, so great that they released a Metro theme for jQuery Mobile