To be fair, I don't think that inclusion in common-licenses is what you think it is. Russ can correct me if I'm mistaken here, but my impression is that common-licenses is around for a technical purpose: to conserve on disk space where many packages share a common license (rather than installing thousands of copies of a given file) as well as save some disk space on mirrors (as individual packages using those common licenses do not need to include the license text, and may simply refer to the file in common l icenses).
Inclusion in common-licenses does not send a signal that Debian endorses nor condemns a given license, only that there are many (the threshold of many in this case is 1000+) packages use the given license. Similar things can be accomplished by doing an analysis of debian/copyright files for packages in the repository (e.g. figure out the most common licenses in the Debian main repository), which would provide more valuable insight as to the proliferation of licenses in Debian.
I think the problem comes down to this:
1. If a license is included in base-files (in common-licenses), then that file is included with every Debian system. This unfortunately also includes other platforms, where it may waste disk space (e.g. mobile devices).
2. If a license is added to base-files, it cannot be removed. This is because, if packages refer to the license file in common-licenses, that file cannot be removed until the packages are all corrected to install the license file itself.
So the 1000+ package requirement is needed to prevent base-files/common-licenses from becoming very large and thus wasting lots of space on constrained systems.
The AGPL is considered Free according to the DFSG [0], [1] - which is about as much of an endorsement from Debian as you can get, or should get. Debian is a nonpartisan organization as a whole, and as long as software is DFSG-compatible, it is welcomed by Debian.
The inclusion of BSD or GPL in common-licenses does not mean the Debian project as a whole "endorses" those licenses, though it would be necessary that they are considered DFSG-free (otherwise they would not meet the 1000+ package requirement in the main repository). That being said, there are many Debian Developers who are for or against BSD or the GPL for various reasons (the Permissive vs Copyleft war has been going on for ages). It is by no means an endorsement for either of those licenses. Heck, the Artistic License is discouraged even by the Perl Foundation due to those aforementioned enforceability concerns, but it is part of common-licenses because of the sheer number of packages that reference it. It doesn't mean people should use it for their own software :-)
Hopefully I'm not completely off-base here. Russ is in a much better position to answer these questions than I am, but having dealt with these issues in the past (for Artistic License 2.0) and having shared in your frustration that a license is not included in common-licenses, I hope that I understand the situation clearly enough now.
Warm wishes,
Jonathan
[0]
http://www.debian.org/social_contract#guidelines[1]
http://bugs.debian.org/cgi-bin/bugreport.cgi?msg=17;bug=495721 (Credit to Wikipedia for this reference, as the Wiki at
http://wiki.debian.org/DFSGLicenses does not mention the AGPL at all)