1. It’s not cross platform.
2. Non-native but mature cross platform toolkits (eg Qt) have spotty support in many of the more recent and popular languages like Rust and Go.
3. The proliferation of the web has lead to application design becoming part of the branding. Which often works against using the sterile native widgets
4. Even before that happened, many companies still reimplemented their own spin on native widgets. Including the OS vendors themselves (Apple and Microsoft are notoriously bad at filling their own style guidelines).
5. A surprising amount of times, native widgets simple don’t exist for precise problem you need solving. For IDE example, you’d have to build your own text area anyway. Likewise for terminal emulation.
6. Web developers are cheaper
I honestly do think VB6 was peak GUI development for desktop systems. But times have moved on.