Some problems include:
* Focused and unfocused windows look almost identical
* Expected features like tray icons, virtual desktops, alt+drag to move/resize windows, even alt+tab don't work out-of-the-box
* Window focus seems completely broken
* Eclipse looks terrible (and I spend much of my time there) - I'm told "no, that's an SWT issue", but it looks great under KDE
* IntelliJ's menus don't track the moue properly - again, probably a Java issue, but still works great under KDE
* Having to "drag" the screensaver thing away is annoying
* gkrellm seems to make all of my window focus issues even worse
I know most of the issues can be blamed on application/third-party framework bugs, but the fact is that I just want to get my work done and KDE/XFCE both work great.
Go look at some of the Gnome source code comments and Bugzillas and you will see the very opinionated "do it my way" thinking that the Gnome developers have. In some cases, it's almost hostile.
If I wanted a desktop that valued form over function, I'd use a Mac.