What's still missing is deeper integration with native OS concepts and programming languages other than JS. Frameworks like Electron are a step in that direction but they come with notable drawbacks. Applications often struggle with things that should feel natural like managing multiple OS-level windows.
Another PITA: Electron apps repeatedly bundle large portions of Chromium, leading to unnecessary overhead. Those duplicated modules lead to bloated RAM usage: every app has its own Chromium copy and OS must keep all that zoo in RAM without a possibility of reusing the otherwise shareable parts.