Actually, I DO remember the first time I saw a Unix filesystem. It was on FreeBSD. And it DID make sense. When I switched to Debian not long later, there was this document that eventually became the Filesystem Hierarchy Standard (FHS). It clearly spelled out where things lived, and in Debian non-compliance with the FHS was a bug (and once the notion of a release-critical bug was invented in Debian, it was a release-critical bug.)
Part of the problem here is that we are in a twisty little maze and every passage looks alike, and our flashlight ran out of batteries in 2013. The manpages, to the extent they exist for things like cgmanager and polkit, describe the texture of the walls in our little cavern, but don't give us a map to the cave. Therefore we are each left to piece it together little bits at a time, but there are traps that keep moving around and it is slow going.
Add to the the fact that it's a damn big cave.
I could understand the FHS in about 10 minutes. This stuff? Would probably take weeks.
The order of magnitude of complexity is entirely different. It came out in the comments on my post that Fedora finally threw up their hands, and the reason that Wifi works out of the box there is because they just expose all wifi passwords to all users of the box. Whoops. Could you have known that by looking at the permissions with ls? Nope. You'd have to read some XML file in a location that network-manager never mentions.