I really don't see why I can't use both. I mean learning JS will be great for me because I will understand the outputted code of emscripten and for managing input on my website. Emscripten would be great for optimized code that is used to make a game. So what do you guys think, should I just learn both and use both where they fit best?
Yup, that would actually be my recommendation! :-)
// Well, except that I wouldn't expect to gain much from looking at the output codegen, since it relies on asm.js and mostly looks like this: