One could reply that it's a feature, since native UIs are more uniform and with less surprises you can concentrate on whatever the fuck you're doing instead of wondering what this app's designer was smoking.

Depends on the UI framework. Most frameworks don't have enough features to make the UI actually good. It's not even about looks, much more about layout. CSS is really good with conditional layout: hide something and everything reflows around it, responsive layout (not just mobile, but also when making app windows smaller/larger). Typography is another issue with a lot of native UI frameworks. Even adaptive DPI support is not yet easy with most native frameworks.

Also things like accessibility. It's quite easy to make web ui accessible, much harder to do it with custom native control.