This should be taken with a pinch of salt because I’m still running RedHat 8, though some things don’t appear much better for the Enterprise version
package manager – I hate downloading new software, because of dependency hell
X11 – I hate trying to SSH into my lab workstation from anywhere, because I invariably get weird authentication weirdnesses
why doesn’t it have a nice task manager like windows?
have they sorted out wireless yet?
what about a media player for .wmv files etc?
there should only be one copy/paste clipboard
why isn’t konqueror designed to behave exactly like Windows Explorer?
Update (April 2007): Ubuntu’s solved most of these issues, but there are still niggles.