The case for the /usr merge

> Of course 'not upgrading' is never an option because i want and must have new features of rest of system - support for new hardware, new editors, new secutiry updates, new architectures, new videos, new internet browsers.

It sounds like you are not using one of the Linux distributions best suited to your needs. Distributions such as debian and gentoo are well suited for an experienced user, such as yourself, who does not want to trade extra integration and automation for additional complexity. With one of those more flexible distros, it is easy to set up a useful desktop system without gconf, network manager or dbus, and without getting stuck on old versions of software. At this moment, I happen to be doing a gentoo install without any of those packages.