I prefer to write in pure JavaScript myself. Some of the reasons are obvious from my response above. Another reason is that I don't "trust" (maybe not quite the right
word) the longevity of the transpiled languages. CoffeeScript, for example, seemed to have all the buzz a few years ago, but now, not so much. Everyone I personally know who used it has moved on (either back to JS, or to TypeScript) and lament the fact that they have CoffeeScript projects to maintain in a language in which they no longer have an interest.
In fact, I do work for a client who has some large CoffeeScript projects set up by a contractor who has moved on, and now he's having trouble finding people to work on them.
TypeScript seems to be getting a lot of buzz now, particulate in light of Angular2, but it remains to me seen if it will stand the
test of time or not.
So, for me, sticking with JavaScript just seems to make sense.
Anyone's mileage may vary, and I urge developers to explore and see what works best for them. But for me, JS makes the most sense, at least for the time being.