The directory structure can be fixed, take a look at heretix(http://www.h-e-r-e-t-i-x.org/, a new linux distrobation, everything is written in ruby(the init system too). The package manager installs everything into /pkg with a name system based on the package name and version. For example GCC 3.4 is installed as /pkg/gcc/3.4/. Then it's symlinked into /bin, /lib and so forth.

At the moment it uses WhiteWater(a bittorrent like protocol) for distrobation. But a change to a new protocol is expected with the next stable release.

Sure there are som problems with their implentation but it is a change for the better and imho the road that alot of distros will take.