While I agree, I think Apple's core demographics does not want to think about the file system. There are enough abstractions created by the apps to the point that users don't think about where their files are at all.
It's not how I want to operate either, but that's the direction Apple has been heading to for a long time
Although they do seem to be backtracking on this stance with yesterday's iCloud Drive announcement [1], giving access to the filesystem they've been trying to hide away for the last few years
what negative aspects of the filesystem would affect an 'intermediate' user (e.g. a high-level hacker) on a day-to-day basis? Admittedly, those two are very frustrating, but I'm struggling to think of any others.
If you Mac loses power and doesn't get to do a normal shutdown, you're eventually going to get file system errors that you can only fix by booting from a recovery disk. I've had this happen numerous times due to a broken battery on my laptop. If you've never ever run a disk repair on your Mac, do one and you might be surprised. You should expect more from a filesystem in 2014.
how about locking my entire system when it wakes externally connected USB drives, namely my time machine. Oddly it seems to occur while I surf.
That and permissions seem to get screwy at times. I had a long running issue where I could not launch JAR files, found others with similar issues and finally figured out, I no longer had permission to my own user folder and the JAR I was launching needed to create a working directory. Ended up solving the problem for more than myself.
I still try to figure out the desire for case sensitivity in about anything
