Your last sentence is specially interesting. Being able to do a "bower install backbone" and going back to work is actually the purpose of a package manager. If it doesn't understand your project structure and is not able to wire the downloaded libraries into your project, whats the point of using it? Then bower is as good as npm or any other tool to download libraries. Right?
What bower manages is downloading dependencies at a specific version and putting them in a folder. It does not wire/unwire them into my index.html. At this point I have to do that by hand. There are a lot of ways my project could be laid out. I might only want d3.js on my dashboard page, I might have a layout template where all of my html imports reside. I might want the files all concatenated together and downloaded in the browser as a single main.js. In it's current incarnation it's still a package manager... it makes packages available at a path. It's just not as useful as it could be if it were a bit more specific about project structure.
