Coffeescript is a dialect for (mostly) people who don't like brackets (also cool but controversial features like null swallowing with ?, implicit function calls, etc.), while babel is a transpiler to take es6 down to es5. Saying one is a substitute for the other is like saying ice-cream mud-cake is a substitute for steak and lobster at a restaurant - if it's Saturday night and or your cheat day, just eat both. That is, pipe the output of your coffeescript into the input of your es6 babel in your build step.
I personally use a ton of emberjs with ember-cli, and ember-cli-coffeescript actually just straight-up ships this build pipeline for you when you decide to use coffee.
P.S.: Sorry if I sound like Marie Antoinette saying "let them eat cake", yes, I realize I am lucky to not have tons of legacy code that prevents me from altering my build step, and that there are thousands of other less-lucky engineers who are stuck with build systems that are essentially unalterable voodoo.
And there's some real benefits to writing in actual Javascript, even if you're still transpiling it for production.
Ultimately, I feel like language choice is something of a bet. And while I like Coffeescript, the future of web development is going to be ES6 and ES7, not Coffeescript. That makes it a lot easier to justify spending time on (writing, learning, etc.).