The directory structure does not help to understand what kind of application is this one. Splitting the code into controllers, directives, services, ... or by pages hides the user cases. The only thing the directory structure is revealing is that this application use some kind MVC pattern, and that is just an implementation detail.

It would be great that when I open a project I see the main user stories/components, and all code related to a user case lies in a single place.