It is hard to find a Linux distro that isn't installed with a default desktop environment anymore. Debians default is Gnome. And has KDE, XFCE and a few others on the install DVD.
Developers didn't get the memo. The base program Samba has no GUI. PeerGuardian by itself has no GUI. You can find a third party GUI for these, but it's not built into them. This creates a problem where the GUI doesn't necessarily match the program it's trying to control.
Another weird issue I've had is that Linux doesn't have OS level controls for setting the proxy. Some GUIs look like they're setting a system wide proxy, but they're not. There's some kind of a disconnect between the people making the graphical desktop and the people programming the OS itself.
In Windows, typing "proxy" in the start menu and configuring the proxy configures it for everything in Windows. Linux doesn't seem to have anything comparable to this. If you set the proxy in KDE, Firefox doesn't automatically know it's supposed to be using a proxy. Apt needs its own proxy configuration as well. This seems so silly. Why do I need to screw around with the command line to do something so basic? This is the annoyance. It's not about typing commands. It's about needing to type the same command 20 times because the OS isn't handling any of this.
using apt through a proxy
Windows/DOS was a disaster like this at one time. Games would come with their own drivers because the games couldn't rely on the OS to do anything correctly. If you fire up Wolfenstein3D, you need to tell it if you're using pc speaker, soundblaster, audlib, or some other sound device. It can't just tell the operating system "Hey, play this sound. I don't care how you do it."-
I seem to recall Warcraft II being the first game I played where I didn't need to screw with the sound and tell it which IRQ to use. I would like to see Linux get to that point with networking. Just have 1 file or command to set the proxy on the entire computer for all users and all programs. It shouldn't be this difficult.