No one in his right mind loves the UI of Jetbrains Apps and the Linux experience has always been a shitshow unless you were using Gnome or KDE. Because Swing does not implement the XWindows protocol properly. So yeah, a great team can still make a functional app with terrible GUI technology -- but there is a world of a difference to something that's really polished, fast and enjoyable to use.
VsCode and atom are simpler, but they just don't provide UI, for many setting you have to go to config files, and some functionality is missing outright.
Can you think of an IDE with better UX?
I like being able to configure just about everything in just a single config file, but still getting an additional escape hatch for overriding OS default keybindings I want to use.
Also, the menu bar in IntelliJ was reimplemented from scratch to make it work properly. The Swing menu bar would have been unusable with its broken handling of submenus.
I suppose preferences here are at least partially determined by how you think about software project management. Eclipse makes perfect sense to me, and has since the first day I used it. IntelliJ is obtuse and odd and ... wrong to me.