Is the problem Javascript or is it that the native environments provide nice and cozy frameworks that almost force you into strong development practices so there is a level of comfort that is generally not found in the browser?

HTML5 is still the wild west, where anything goes. "jQuery spaghetti" is considered acceptable by many, and to convince developers who write in that style to provide structure to their application is asking them to do what often pushes them away from native development in the first place.

Once you build up a solid MVC (or similar) framework in which to develop your Javascript/HTML5-based applications, the differences between native and HTML5-based development seem pretty trivial to me, and a few syntactical differences between the languages used on the varying platforms are no more than a talking point.

If you dislike JS so much, why don't you use some cross-compiler?