First of all they're not the same thing. Coffeescript transpiles to JS (ES3 or 4 if I remember well) and ES6 is a new standard (not finished yet). Maybe one day coffee may compile to ES6 (but that's not likely since that would break support with older browsers). As said before, ES6 may reduce the need of transpiled languages but won't replace them. From my point of view, ES6 will never replace ClojureScript nor TypeScript (ES6 doesn't bring the power of a LISP like clojure or the type system of TS). As for coffee, many people may still prefer its more lightweight syntax that ES6 does not intend to replace either.

Let's say that ES6 will provide a better runtime that may make transpiled languages less useful. Yes, ES6 does arrow functions and classes but it also provides many more cool stuff that the transpiled languages may never support such as generators if they intend to keep backward compat to older browsers. If you are in this case you should bet on ES6. If you don't care and are happy with what's included in coffee, use coffee ! You can always compile it to JS and continue your project with ES6 !

To sum up, transpiled languages are not dead and are still way more flexible than vanilla JS (as they don't depend on a big specification such as the ES specs) but ES6 does improve the runtime, and one day transpiled languages may use this new runtime.

I think that ES6 is going to reduce the need for things like CoffeeScript, or at least a lot of what people use (arrow functions, for instance).