First off, Unix is not Microsoft Windows. If you try to shoehorn a Microsoft Windows paradigm onto Unix you will have difficulty. The reverse is also true.

Allowing arbitrary users to modify another user's configuration is considered a no-no in Unix land. Modifying system-wide configuration is the same as modifying another user's configuration. Not allowing this is a good thing. When in Rome, do as the Romans do.

Also, keep in mind that outside of /home and /var, it's possible (and even likely on installations like a smartbooks or MIDs) that filesystems are mounted readonly. Trying to write to such a place is likely to bring you woe.

That said, system-wide settings go in /etc. You need to be the root user to write to /etc, and you need to be the root user to install software packages that are available system wide. I do not see the problem.