It does have some advantages, but the author of a library creates a library to do a specific thing and to do it well. When it gets added to the language, as we've seen with the horrible module proposal, lots of people all disagree on how it should be implemented so you end up with a much worse implementation than if you just let individuals create the feature how they think is best.

With libraries, you are free to switch to other ones if you don't like the way it does a specific thing. Don't like CommonJS? Don't use browserify, and instead try RequireJS. Don't like how Prototype extends the prototype of objects? Try jQuery.