1. Hidden files. Why? If the file merits existence, it should be seen by the user. Many hidden files, such as .htaccess, contain critical configuration settings that must be modified to get things to work. Just stop it with the hidden files. Probably fifty million man-hours around the world have been lost because some developer thought it was wise to hide files from the user. This is anti-social sadism on the part of developers.
2. This infernal pop-up which arises in every Linux program. Trying to edit a text file from within a program like Filezilla is impossible. Instead, one must drop to the command prompt, because the Linux GUI is useless. Even if one does, somehow, track down the location of the text editor using the Browse button, Linux permissions will not allow the saving of the text file. Potential time lost? 5 - 10 minutes per attempt to edit a file. In Windows, I can load a text file from any program using Notepad++, and it takes me approximately one second to do so. Why is Linux retarded?
3. Networking in Linux. I hate networking above all other things. But Samba is a program that is confusing in the extreme. It is designed for a server, which means it is about a trillion times more complicated than necessary for a home network. What do all the settings mean? Why do I need or want to enter a password to access a directory on a networked computer at my own home? Why is everything so slow on the network? Why isn't there some kind of GUI? Over the years, I cobbled together a configuration file for Samba that I use in every Linux distro. I spent many hours sweating over that thing, trying to figure out what it all means, but I still don't understand half of it. I don't envy the new user to Linux that has to figure out home networking for the first time.
4. Muon. I don't like the Kubuntu Software Updater or the Kubuntu Software Manager. I can't find the programs I want in them, for one thing. In keeping with the general Linux philosophy, the program I want are "hidden". I can find the programs I want in Synaptic, but not in Kubuntu's programs. As for Muon Software Updater, it's buggy. It used to be a lot buggier, but it still has strange problems. Synaptic just works all the time, on the other hand.