But compared to the web, native applications are significantly worse in these areas.

Especially on that first point. I can go to the vast majority of web apps on just about anything with a browser and get it up and running in less than a second knowing nothing more than a domain name.

And there's "cross platform" then there's "cross platform". Something like QT is amazing, but you are still looking at the big-3 desktop OS's, and maybe the big mobile guys if you work for it. A web app includes all of that, plus my TV, my car headunit, and even my damn watch! (I often use a web home-automation app from a browser on my watch, the UI adapts pretty damn well for quick light-flips)

Nothing is perfect for everyone, but just because it's been done since the 80's doesn't mean it can't be improved on. And as always it depends on your actual needs. There aren't any "better" and "worse" architectures.