How about this for an idea?
A minor alteration to the installation process (and it would even be possible to download a 'converter' so that your current system could benefit):
When you install a package, the package contains all of the information about where to place the various files. There are certain standards which are usually adhered to, such as binaries in /usr/bin, documentation in /usr/share/doc, and so on. Now, what I propose is that we add a little function to dpkg so that some soft links are created in some other directory (/software for example), while the actual files are stored in the usual place. For example, lets say we have a package which has the following files and their target directories:
Why can't we keep this structure, but ALSO create a software directory which only contains LINKS to files, but uses the package's name? For example, the structure of the software folder would look like this:
convertor ---> /usr/bin/convertor
conv_lib.so ---> /usr/lib/conv_lib.so
README ---> /usr/share/doc/convertor/README
COPYING ---> /usr/share/doc/convertor/COPYING
convertor-logo.png ---> /usr/share/pixmaps/convertor-logo.png
Now granted, given the nature of free software, programs tend to share stuff, which is why the current system is so beneficial. Theoretically, this new system is a 'waste of space', even though we wouldn't actually have multiple copies of the files, we'd just have multiple links to the files. Even though we're wasting space, we're wasting a very, very minimal amount. This method also means that compatability isn't an issue. Developers don't need to worry about the new software folder, because everything is sorted out by dpkg.
||||||/convertor (the root of the package's directory would contain a soft-link to the binary)
||||||||||/doc (this directory would contain a soft-link to the various documentation files)
||||||||||/lib (this directory would contain a soft-link to the various libraries required by the software)
||||||||||/data (this directory contains miscellaneous stuff like images, sound files, videos etc)
At the end of the day, the current system is fine for me, but I think that we should have the CHOICE of a different system. As I've just shown, there's no reason why we need to get rid of the current system, or even why this should be a difficult task to accomplish (because it really isnt, it wouldn't take much work at all). Obviously, the current system is not ideal for some people, and if they've only used Windows in the past, then it's pretty obvious that they may be thrown off by the directory structure which Linux uses. I see no reason why a secondary 'fake' directory structure couldn't be included as an option when first using your new Ubuntu machine. For the hard-core efficiancy junkies, they can just leave the feature turned off, but for those who like a more centralised structure, they can enable it and then be satisfied.
If something like this were to be adopted, however, we would still need to keep the new directory structure outside of the home folders, otherwise we'd have as many duplicates as there are users, which is just pointless. Anyone wishing to edit stuff inside the new software directories would still need to use root priveleges.