In my experience Babel minified better than Closure Compiler with less maintenance of the externs on my part.

Dead code removal relies heavily on writing JS in a style that allows for static analysis. Dynamic requires, heavy usage of closures, knowledge of external/global variables are all things that prevent a lot of commonjs code from being removed. https://developers.google.com/closure/compiler/docs/limitati... has more information if you're interested in the assumptions that the compiler makes.

Interestingly, we're finally starting to see these ideas get more mainstream as people adopt es6 modules and publish bundled code with explicit externs in tools like Webpack 2 and Rollup.