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.
There are some more coherent arguments in play, don't get me wrong (in particular, the argument that web apps are a bastardization of what the World Wide Web was intended to be for; I agree with that wholeheartedly), but a lot of the rhetoric around here really reeks of elitism.
"It seems like the majority of the comments opposing web apps oppose them because they're cross-platform and not written specifically for their chosen platform, which is a very silly stance to have."
But it's not. By not being written specifically for the platform, everyone is just getting a least common denominator approach. Nobody is getting anything that integrates with their platform. Nobody is getting anything that embraces what makes the platform special, or good.
"but a lot of the rhetoric around here really reeks of elitism."
No, it's more that we want developers to actually make an effort to embrace the platform they're trying to work on. And, quite frankly, use something that's not JavaScript. Learn a second language.