There are a lot of desktop usability issues in Ubuntu IMO. I do feel this is the best Linux end-user distro, but is a far cry from e.g. Windows or MacOs.
Here are a few issues, both usability, aesthetics and general linux issues:
1. Unity launchpad placement is awkward on the left. No possibility of moving the launchpad to bottom or customizing it in any manner.
2. Not possible rearrange the order of the icons in the Unity launchpad.
3. All instances of same application are stacked together, so it's not possible to select directly from the unity launchpad the instance you want.
4. Alt-tab disables the mouse.
5. Alt-tab stacks multiple instances of same application, so you need to first stop on the application for it to expand it...and even then the presentation is awkward.
6. Alt-tab does only show icons, but not live window capture.
7. Almost no possibility of customizing the look n' feel of the GUI. There are no alternative themes to select from, nor any way of modifying the theme easily.
8. Showing menu of an active application in the topmost bar makes no sense. I'd rather use that area for launch icons and move application menu to the application window.
9. Ubuntu does not help you install correct video card drivers after install.
10. Difficult to resize a application window, the border is too small. The resize cursor icons ugly.
11. The compact scrollbar is bad.
12. The toggle button is confusing.
13. Filesystem structure is confusing. You have no idea where an application is installed or things are.
14. Defaults fonts are not good enough. I switched to OpenSans. Some text on web pages looks awful, and I see lot of "clipping" and overflowing.
15. Not possible to minimize all windows except current, e.g. window-shaking like in Windows.
16. Inconsistencies in the UI. Try right-clicking in the web browser window, see how the context menu looks like. Then right-click on the desktop, and then right-click on a icon in the launchpad. 3 different look n' feels!
17. I feel like the UI is bulky, and that I have more space to work with in Windows.
18. Ubuntu does not help you discover nice tools to install, you need to know exactly what you want. There's also a lot of garbage in the software center.
Some can be fixed with tweak tools, but if I want to change anything more I feel like I need to spend a lot of time researching it, and do something I feel "hacky".