It's not a matter of expertise and attention to detail. It certainly isn't impossible to make a native-feeling web application, but I do think that the level of effort is comparable to just doing the app natively, and the web counterpart will still fall a bit short. For what it's worth, WinJS apps still feel clunky to me when compared to their native equivalent.

I think summarizing responsive design as adding media queries oversimplifies things a bit. The test overhead for PhoneGap is enormous; deploying fixes to an app is much more difficult than deploying fixes to a site, and individual devices can exhibit bugs that other devices won't within the same Android version. Adding different levels of responsive layouts multiplies that effort. By the end of one particular PhoneGap project, I literally had a dozen different devices on my desk to assert reasonably small changes.

The browser as a leaky abstraction thing also continues to be a pain point. One particular difficulty I had with PhoneGap was Android 2.3.x, in which div overflow scrolling isn't implemented (also, ironically enough, not implemented in WP8 IE10 when used in conjunction with the -ms-viewport CSS rule), requiring a design that either doesn't use scrolling elements, or emulates it with JavaScript. In either case, the native experience wins out.

Hitting several platforms with a good-enough experience may be an overriding priority, and you could certainly pick worse than PhoneGap to make that happen. For my own tastes, though, I'll be leaning on Mono for cross-platform efforts.