Native apps generally have nicer UIs, better performance, and reduced resource-consumption, and may have more features.

All true except reduced resource consumption, I don't believe that's an universal truth. Some native apps drain a lot of battery because they do more than they should, like the Facebook app spying on you on every conceivable way (and probably also in some inconceivable ones).

Technically I covered that under "fewer features" ;-P

Surely it is the other way around?

Apple will reject your app from the store if you ask for permissions not necessary for it to function. It also gives the user fine grained control and awareness of what the app has access to, for how long, etc.

Some random JS app that can load in whatever it wants after the fact can make no such claim to as much security or privacy.

Whatever JS a page loads it cannot steal all my contacts, browse my filesystem or track my location without me giving permission, so I consider web apps much better than native apps privacy-wise.

It's true that Apple does a better job at protecting the privacy of its users. I'm an Android user and privacy is terrible. I self-limit myself to use the least amount of native apps, using webapps and open-source apps as much as possible. For example right now I'm using Hacker News through it's web interface on my phone.