As we are moving to HTTP/2 and JavaScript heavy applications are everywhere we should stop bundling all of JavaScript files into a single big bundle file. It will help with caching a lot because right now we update the bundle if a single line in the code base changes. A lot of front-end build systems are optimized for HTTP/1.1.
There's also the fact that some browsers (IE on < Win10) will languish for a few years, so you may still need to support them, to what extent, who knows. And until there is proper support for native module loading in the majority of browsers, we aren't likely to see separate files widely adopted again.
Beyond all of this, as stated above, caching really hasn't worked out so well in practice, and shouldn't be your main optimization unless you are building an internal application that your users regularly utilize... Of course, those are the environments most likely to let best practices slip in terms of meeting deadlines.
So, the big resulting file is not a "bundle" and can't easily be split into parts.