An actual list would be long, nuanced and vary by platform, but I'll offer a sampling.
For many things there's might be a basic API available, but when you dig a little deeper you find huge limitations. Geolocation is a great example of that. Sure, it's available. But you couldn't implement a navigation app, for example. Because you can't watch the location and get updates in the background. Not to mention that accuracy and update frequency can be severely reduced in a PWA vs a native app.
Other limited APIs include things like bluetooth, audio, NFC, notifications, file system access, sensors (proximity, light, etc), camera functionality.
Safari (and therefore Apple) doesn't support things like accelerometer/gyroscope access, battery status, vibration, network info.
You can't access things like the user's contacts or calendar. And we could argue over whether limiting access to stuff like this is a good or bad thing. But the fact is that this stuff is available in various ways to native apps, but not at all to web apps.
As an app developer, if the app is nothing but images and text and the full experience is just a series of json, it should be a website. Those kind of apps are the most boring to work on.
But our phones are more powerful than the computers that landed us on the moon and are packed full of sensors and connectivity. The web is incapable of matching a native app, if it is actually doing something interesting.
Outside of games, very few apps are doing anything interesting. The only reason for them to be apps at all seems to be to get a place on your Home Screen and to push notifications.
A website in your phone browser will not be able to see when you're leaving work (or a friend's house, vacation), calculate when you will be home, turn on your HVAC, raise your garage door, and unlock your door as you approach the door.
It also won't display the weather for the next few hours and your calendar on the same screen whenever you open up your phone without being an extremely bothersome action every time.
For many things there's might be a basic API available, but when you dig a little deeper you find huge limitations. Geolocation is a great example of that. Sure, it's available. But you couldn't implement a navigation app, for example. Because you can't watch the location and get updates in the background. Not to mention that accuracy and update frequency can be severely reduced in a PWA vs a native app.
Other limited APIs include things like bluetooth, audio, NFC, notifications, file system access, sensors (proximity, light, etc), camera functionality.
Safari (and therefore Apple) doesn't support things like accelerometer/gyroscope access, battery status, vibration, network info.
You can't access things like the user's contacts or calendar. And we could argue over whether limiting access to stuff like this is a good or bad thing. But the fact is that this stuff is available in various ways to native apps, but not at all to web apps.