If you are someone who jumps between Windows, Linux and macOS using the same app then consistency in how the app works is a big gain for you, and then the impedance comes from the system you are using.
I didn't mean to imply that Java apps are bad, far from it. Many java apps are good, they just stick out like the proverbial, and performance historically was not as good as native apps. There was a time when the go to torrent application was java based and Netbeans and Eclipse were the IDEs of choice. But they made trade-offs, and two of the key ones are performance and consistent UX with the operating system. For many applications / users, this is a fine trade off to make. But Atom made a similar trade off and then the developers have spent all this time and effort trying to improve performance, and that is what I was trying to be snarky at, that its obvious why performance will always lag.
And regarding Java application speed, IntelliJ is pretty much comparable with the "native" Visual Studio.
About the looks, I'm using right now Vim (GTK), Skype (I don't even know what toolkit it's using, but I'm pretty sure it's not native), Eclipse (SWT - sort of native), Pidgin (GTK), Firefox (XUL? I'm not 100% sure after 57), Chrome (Skia?), etc.
Users don't really care as long as the applications are useful and developed properly. I've used many crap and butt-ugly "native" apps...
I don't even use Atom, but this vitriol annoys me.