I've worked with both, ES6 is definitely a big progress on Coffeescript, but it takes like 80% of the things from coffee IMO, except the indentation syntax and list comprehension, added an `import` keyword.
My point is: don't complain about coffeescript while cheer at ES6, they are mostly the same.
Except... CoffeeScript does all sorts of nice things that Babel does not. List comprehensions. Lack of == operator. Correct modulo operator. Block regexes. Triple-quoted strings. The @ syntax.
There is a strong cult-like vibe to the JS community, and I really find it off-putting. They have taken a technical limitation "Browsers only support JS" and turned it into a socially enforced rule "You may only use JS". Fuck 'em.
No, they are really not.
ES6 does not change the semantics of the language. It adds a couple of new useful features, but it still maintains the basic readability of JS.
I've written production apps in both. With Coffeescript, I regularly encounter problems where the generated output is not what I expected given the input and the only way I discovered that was examining the output JS.
With ES6/Babel, I have literally never inspected the generated output. It's never produced code contrary to what I expect.