Your last paragraph basically describes a browser with a special "install" flow. Mobile Chrome already has a flow like that for PWAs where it will ask you "do you want to add this to the home screen?" and it will add the icon to your app drawer on android just like any other app, allow you to "uninstall" it just like any other app, and when you launch it it launches fullscreen just like any other app.
I'd love to see this expanded to cover desktop as well. And with some additional work (like giving the option to move storage data to different drives or manage apps based on their hostname more easily), it could become a very powerful system.
If you want to learn more, take a look at the google developers page for PWAs. It seems to be what you are looking for in some ways!
>I think we can work with those benefits, and give users and developers the options needed for other formats if they want.
That's literally what I'm advocating. Not getting rid of webassembly applications in the browser, but also having native runtimes that are optimized for running the same webassembly applications.
Every benefit that the browser as application model provides could improve the way native applications work as well - there could literally just be a button or an option in the browser to "install as native" and the Webassembly binary in the browser could just be copied somewhere, maybe with some metadata, and an icon generated for the desktop. Native runtimes could sandbox them just as a browser might, and the uninstallation process need be not much more complex than dumping a cache or deleting a folder.