If people _insist_ on making phone apps as websites, there's Cordova and all that. Such apps are never very good, of course. I still haven't seen a website-based desktop/phone app that wasn't a clunky non-native-looking resource-hogging mess.
Why not? Because they can actually be extremely useful. Such as for receiving emails, Facebook messages, Slack pings, or news updates you've subscribed to. Maybe somebody tweeted you. Any of these apps could work as progressive webapps.
Regardless if the platform is native or web-based, the feature remains opt-in. If you don't want them, then don't subscribe to them.
I think it's valuable for games. Unity and Unreal engine have demonstrated that.
Applications necessarily intersect with the underlying platform in a way which games do not. Accessibility, system-wide services (e.g., dictionary), system-wide interactions (e.g., drag and drop). There are reasons I choose macOS, and when applications embrace the design philosophy and features of the platform they become great applications. PWAs will not do this to the same extent (and if they try to, the effort would be so significant they might as well go native).
I feel strongly that the platforms you develop for should be the platforms you love using. And so the things you develop should bring out the best and most valuable features of those platforms.
I would rather encourage developers to embrace each platform's strengths. I understand that many companies might not care — they want as many users as possible as cheaply as possible. But I do not appreciate that attitude at all.