http://david.heinemeierhansson.com/2012/rails-is-omakase.htm...
http://david.heinemeierhansson.com/2012/rails-is-omakase.htm...
CoffeeScript was basically the logical complement to Haml (Ruby-like syntax for HTML) and Sass (Ruby-like syntax for CSS) -- although Sass has since dropped its original syntax and moved on with the CSS-like SCSS.
Since then CS has lost a lot of popularity outside the Rails community. Babel and TypeScript provide similar syntactic niceties based on actual additions to the language (Babel is basically letting you use unfinished future additions to JavaScript before they are actually implement or even published). Sass in many projects has been replaced with libsass used via Node.js bindings. Entire toolchains like Grunt, Gulp, Browserify and Webpack have sprung up around Node.js. Not to mention that universal/isomorphic apps are now a thing and anything nontrivial generally assumes you're using a Node.js backend.
The default Rails stack is precisely that: a Rails stack. Rails is backend software. It has been around long enough to have seen the massive changes the frontend has undergone from being basically "just some assets" to an entire ecosystem of its own right.
The Rails asset pipeline is simply not sufficient for any serious frontend project anymore. This is not Rails' fault. It's just a natural evolution all backend software has observed. Rails is still a good solution for building API servers or even simple frontends. But it's not a complete solution anymore and it can't be.
In time rails will need to replace this out, as the JS tooling keeps evolving, better solutions will arise.
While I wouldn't use vanilla rails & UJS much today, I still think it has value in getting things going.
I'm fairly certain there's not much of a point having jQuery in Ember and there's certainly no point in using it in jQuery (unless you just blatantly append random UI libraries -- most jQuery UI widgets can be implemented with fewer lines of React).
Most sites require jQuery, most developers are happy using it, why put the effort into getting rid of it?