Interesting recurring topic indeed, thanks for sharing.
I am also thinking trees have a lot to offer, plus the advantage of not preventing anyone from using tagging or categorization & taxonomies.
I think facets are another beast though, purely intended to be used for Search & Find. I would not really consider them as a solution to organize our content upfront. Are they?
It’s also interesting to see how FS and other software (beside CMS) are evolving. FS UI, which are per definition trees, are less broadly used by end-user apps. Apps such as iCloud, GDoc, IA Writer, the Mac Finder and many others are more and more trying to leave the concept of “physical tree” to get to something more based on meta-information, that can also be a virtual tree sometime but with different // organizations. From a UX standpoint, trees have a lot of flaws, as you mention it.
To be continued…