It's nothing to do with JS code execution, the problem is in the rendering engine, essentially too much repainting and rendering stalls, and too little GPU accelerated animation paths.
Javascript is in a very good state these days in terms of cross browser compatibility, and while CSS support has converged between browsers in terms of correctness, CSS support has not converged on performance between browsers. Safari, Chrome Firefox, and IE have wildly different animation performance hazards on the same markup and debugging this often isn't trivial, for example, finding out that the GPU is stalling on texture uploads deep inside of the render loop.
One bright point, is that apps like Inbox are forcing these issues to the front, as is libraries like Polymer/Material Design. As the issues are raised and fixed, jank free rendering on mobile web platforms improves, hopefully reducing the need for native apps.