I think it all stems from D-Bus, which has become the primary mechanism of command and control on desktop Linux. To address the OP's initial issue of user mounting disks, it's managed via Udisks, which is mostly accessible via D-Bus.
I have trouble reconciling Unix's notion of "everything is a file" and how a modern Linux desktop operates via D-Bus. Don't get me wrong, I think D-Bus very powerful and flexible. I just wish it was easier to explore and test via file-based tools. Maybe a FUSE layer?
Anyhow, if the OP thinks that Linux was once "clean, logical, well put-together, and organized", I can only laugh at his rose-colored glasses. Linux is and always was a cobbled-together mess of orthogonal paradigms (no better illustrated than by the design philosophy clash of XWindows vs Unix). Maybe earlier Linux was simpler because it was still playing catch-up with other Unix clones out there. Nowadays it's leading the pack in innovation, and so things are changing, and fast. I don't know if documentation really is worse now that it used to be, I'm afraid to fall in the same nostalgia fallacy.
Ultimately, I see this rant as nothing other than "things are different now and I'm scared and confused". Not that I don't sympathize, being in roughly the same place. However, I decided I can't stop technology, and sucked it up and sharpened my google-fu.