The advantage of web applications is that you do not have to install and update them, that they are inherently sandboxed, and that they are not operating system depended. And even those are not universally good things - server down or no internet connection, no application, feature removed in new version, good luck trying to run an old version, and operating system dependencies give way to browser dependencies. And you have turned even the simplest application into a distribute one unless you put in the effort to make it work offline from the browser cache.

Everything else is worse because you are forced to use this single technology stack that the browser offers you. And people are trying to break free of those limitations, WebAssembly, WebUSB, or doing their own rendering into a canvas instead of having a DOM. One size fits all was, is, and will never be true. Are there certain applications that benefit from being web applications? Sure. But is this a panacea? Certainly not.

At some point you browser will just turn into another operating system running on top of your operating system. The success of the current situation is, I think, mostly due to the fact that the web browser was a universally adopted least common denominator for running arbitrary code. You could get all the benefits of web applications without the browser, you could have platform independent binaries, you could download them on demand, you could sandbox them. But you probably would have a hard time to invent those standards and get them universally adopted by all platforms and operating systems.