Things you can't do with a GUI:
- you can't manage advanced power management profiles
- you can't manage devices
- you can't manage services
- you can't manage firewall in GNOME
- Device Security is almost useless
- There's no versioned backup system that does both user files & system snapshots integrated into the Desktop Environment and the DE settings app.
- There's no DCONF equivalent for KDE (that I know of), the need for DCONF shouldn't even exist.
- No integrated, easy to use & performant remote desktop software (VNC is not enough, RDP in GNOME just doesn't work, Sunshine is a pain to setup)
I'm an Arch user, so I'll talk about it below:
- There's no real GUI for Pacman, Pamac is known for horrible stuff. Alternatives are very inferior.
- There's no GUI for system updates integrated into the settings app
3rd party crap:
- Nvidia (nuff said)
- Flatpak (convenient, but it's still a mess)
Props to:
- AMD, I love you guys.