Per the distro's FAQ,

Did you redesign the tree to make it more newbie-friendly?

No. In fact, it was motivated to fulfill the needs of users who prefer to install applications from the original source packages instead of relying on the distribution. That is the main reason why each application gets its own directory: so you can install it from source there and then remove it with an "rm -rf". So, you see, GoboLinux was designed focusing the experienced user who doesn't like things to be automagical. Our scripts merely automate procedures, but they don't "make decisions", and whenever they have to, they ask first. The binary package collection was created as a way to avoid duplication of effort between users. The Compile project was created to store "compilation rules" of the original source packages of the applications, given that there is no single standard on how to compile apps on Linux. We do not wish to estabilish a "packaging standard" such as RPM. We think that there is no real need for "packages" if the original .tar.gz is properly made. For instance, when an application uses the GNU AutoTools (autoconf, automake...), compiling for GoboLinux is trivial; for non-trivial cases, Compile takes care of accumulating the necessary knowledge on how to compile things. However, given the more logical directory tree, GoboLinux is often considered a more conceptually friendly distribution, as its structure is more logical and less hindered by historical limitations. But we do not target beginners as a specific goal (at least not in short or mid term).

Basically, GoboLinux is oriented towards people who like to compile their own software, like the filesystem layout (I've been reading the docs and definitely want to give it a shot), and don't like software that tries to figure everything out for them.