I think there's a distinction between an HTML App like those made with PhoneGap/Cordova and a Web Application like Gmail.com. And I personally don't think that's a bad thing to restrict most of those APIs from Web Applications. Do I want or need a webpage to be able to turn my Camera Flash on and off? Nope Nope Nope.

I think a lot of the newer APIs being exposed to the Web via the Browser are not very well thought out and will eventually be removed because of the risks they present.