I would recommend using Yeoman for seeding projects. The grunt system it uses will solve the "lots of js files" in main page problem by automatically concatenate files together.
In our project, we created multiple sub-directories underneath the controller and services folders to organize them by business functions. It's fairly easy to re-organize the file structure in an angular projects.
In our project, we created multiple sub-directories underneath the controller and services folders to organize them by business functions. It's fairly easy to re-organize the file structure in an angular projects.