Disclaimer: I like web browsers, I just don't like my apps running inside them when I have the option to go native :D

In my career, I have built a handful of PWAs and many native apps, so here are my two cents on web apps.

The web browser is terrible for anything more complex than a simple HTML site with a few dynamic elements. It offers:

Subpar UsabilitySubpar Usability

• Different browsers have different rendering engines, so what looks and feels good on a new iPhone running Safari might not (and probably won't) look and feel the same on my old Xiaomi running Firefox Nightly. To be fair, this is also the case with native apps sometimes, but the differences are more subtle and more manageable.

Terrible PerformanceTerrible Performance

• Even poorly coded native apps easily blow PWAs out of the water;
• Most browsers take several seconds to load on low-spec devices. Stacker News takes as much time as Twitter to load on my device, which is between 15 and 30 seconds.

Terrible SecurityTerrible Security

• Lack of secure storage (see @koob's answer);
• Your code runs on a browser, which is a slow beast more complicated than a full operating system, so who knows what's happening in runtime. Of course, the same could be said about native apps because they run on top of complicated operating systems, but at least it's one layer less than a PWA, which introduces an additional layer by running within a browser on top of the OS.
• Etc...

Terrible Developer ExperienceTerrible Developer Experience

• Buggy tooling;
• Terrible debugging experience due to JavaScript;
• TypeScript offers better debugging capabilities but is not a language I would call good.
• Etc...

Maybe WebAssembly will fix these issues (except for slow browser loading), but then what's the point? Why not just make it native instead.

Also, HTMX is really promising and might help with some of the issues above.