You points are as good as one can think of. But please consider what Debian is working for. The want to be fully conformant to whatever Standard will be there for files and directories. Now one of the points is. No vendors should install anything below /usr/local. The point is if you make it easy to instal whereever you like. This will be done and all the work on standards will go downhill.
If you aren't just using Debian, then you'll see how different the other Distributions are. Config-files in non-standard places, cluttere all around and that with the x GB files which a Linux distribution consists of nowadays. So you can't be sure on different Linices (plural?) to find what you're looking for easily. Just my 2 cents Friedrich -- for e-mail reply remove all after .com
