Qt also "uses native widgets". It doesn't matter, it's still wrong. Yes, the buttons have the right pixels, but nothing behaves exactly right.

I think it's actually worse feeling than a toolkit like GTK+, which is more of a Linux toolkit that "happens to work" on Mac OS. Qt apps feel like they're trying to sneak something past me (except on KDE, of course), and there's a very uncanny valley-esque effect. A GTK+ application is more "upfront" about it, so at least I understand what to expect immediately.

Cyberduck, a file transfer application, is written in Java, but I had no idea because it uses actual bindings to Cocoa. If you want to provide the best user experience in a Java application, that's the way to go, write swappable front ends for each operating system with the native toolkit bindings.