1) The GUI is incomplete: look at the preferences, for instance. To change a setting, you have to open the defaults settings file, find the setting you want, copy it into a different file (user settings), and change it there. Actually, I take it back: it's worse than Emacs in this regard.
2) What GUI is there often works strangely. For example, if you open a folder you get both a sidebar and a tab bar. You can put files in the tab bar by double-clicking them, or you can browse the directory in the sidebar. But if you select a file in the sidebar which is not open in a tab, you end up with a tab bar with no selected tabs, which is quite jarring, since tab bars in all other applications always have one active tab. If you only have one tab visible, it looks like it's active even if in fact you have selected some other file in the sidebar (the fact that active and inactive tabs look very similar in the default theme does not help).
3) The default theme gives you a window that is a strange mix of light gray and dark gray, with no apparent logic. It looks like parts of two different applications got mashed together. I have yet to find a theme that looks satisfying.