The problemCSS was invented for designers. But do you really know that much designers that are able to provide you with a nice CSS rules that will be awesome on all screens? You are favored by gods if it is your case. Most of the time, they will provide you with some PSD (what an ugly form of design), AI (if you are lucky), Sketch or SVG (here, it is not anymore based on luck, it is like having an angel upon your shoulders).
The same goes with HTML. Semantics that appears with HTML5 were added for SEO. But do you know that much SEO guys that will give you the right HTML code? I haven't seen any in my whole 20 years on the web carrier(though SEO is not that long of a job).
Thus, why are we using 3 languages for writing our codes. Is that right? Do we have to? Is it done for helping us and keeping separation of concerns? Funny. Patterns like this exists since the dawn of design patterns from the GoF. And what if we need to synchronize this HTML, CSS and JS back together for animations purposes? We request back in our code the HTML tags that we have just declared? We hooks on the CSS? If we need a color theme, do we have to write it twice or more? Funny, too. Even media queries for responsive web designs, seems like an odd way of reproducing the abstract factory pattern (or the bridge depending on if you know to who you are distributing your files).
The solutionsThere are many. Generally, I was keen on using preprocessors: SASS, LESS, Stylus, YAML, Jade, Blade, CoffeeScript, Typescript, Dart, ... But, it finally does not give me a proper answer to the problems previously mentioned. It still need glue code to make all of this work together properly. Things started to shape up when I end up using Meteor, Famo.us and Velocity.js. The Blaze component of Meteor is transforming your HTML, more precisely, your HTML templates using Spacebar, a derivative of Mustache, into JS code. The same goes with Famo.us. It creates HTML and CSS rules that plays well together so that they limit layout trashing issues and combines this technics with advanced physic and animation engine. The same goes with Velocity.js. This jQuery plugins brings back synchronized CSS animations in with JS.