For example, I tried to config gpsd to use another port, nothing would work; systemd quietly overrides gpsd's configfile and required additional systemd incantations to change what should have been easy. And the man pages are a mess
And journalctl makes me want to pull my hair out; just let me grep a regular file - discovering namespaces is a nightmare
ls has more flags than a Soviet military parade.
Some programs can crash when all their files are suddenly swapped for new ones. I've seen multiple linux systems bork themselves during an update because the update itself caused the desktop session to crash, which caused the update process to be interrupted just as it was modifying some crucial files, thus rendering the system unbootable.