"Transpiling" may never go away, but it will cease to be the first thing everyone reaches for when web assembly comes out and reaches the point you can use it. It's the first thing right now since it's pretty much the only thing. Web assembly will pick up a lot of the use cases. Something like Coffeescript will probably still target JS by design, something like Emscripten will tend to target web assembly, and where the in between will end up is anybody's guess.