Ok, then how about the fact that CS is much more of a functional language since everything is an expression. There are other semantic advantages. Also, isn't everything, including features in ES6, just a preference thing? You could prefer to write in assembly language. This whole discussion is about language preference.
I only know of two. The debugging issue and coffeescript-haters (I use that term loosely) not contributing to coffee-script projects. Pre-compiling is a non-issue. I don't even know it is happening. What am I missing?
BTW, did you see the thread about my project attempt that gives ES6 a syntax wrapper with CS syntax? It would not be a trans-compiler, just syntax converter. I would switch to this if it existed even though I would lose some semantic features. It would solve all problems including the non-contributor problem since it would be two-way and allow one person to edit with the wrapper while others see clean ES6.
Unfortunately I am stuck on the two-way feature at the moment and it may not be possible. My current solution adds a lot of superfluous git changes. Without the two-way feature it isn't worth doing.