Why the [system] directory?

[eluser]louis w[/eluser]
Personally I prefer the system directory inside the application one. Because of the fact that the system directory contains all of the base CI code, which shouldn't be changed, I like to get it out of the way. I also have added a directory inside application called assets which houses all my js, css and images. I keep these inside the application folder because I manage them with a asset manager self built library.