The separate-by-feature approach gets a much better treatment in ngBoilerplate: https://github.com/ngbp/ng-boilerplate
Remember when starting a new web project meant opening a notepad and writing some HTML? Yeah, well I spent 4 hours diving into this boilerplate project yesterday and still haven't gotten it right for Angular development and deployment.
Try to start a project with angular, coffeescript, and requirejs. On top, have the audacity to not want to use array syntax but have ngmin deal with that.
You're in for a world of pain. 4 hours did you say? I've been working on this (in free time, granted) for about a month. It took me a while to believe this isn't solved already. Apparently the angular-seed world and surrounding tooling stil has way to go.