1. 3D Touch is supported through the Apple Webview API.
2. Touch ID can be integrated using a native plugin.
3. Apple pay through plugin should be available with iOS 10 web api.
4. Cross app communication is possible through URL schemes.
5. Size classes are provided by native iOS and should be supported by phonegap. However, I do not believe phonegap provides a way to implement size classes for iOS if thats what you meant.
6. Sure it does.
7. Siri integration for apps is not yet available since SiriKit will be shipped with iOS 10 for developers.
8. Yes offline mode is supported.
9. The new features are usually available soon after a new OS is released.
A few things I thought I'd add to @vishal_mishra's already excellent answer:
1. 3D Touch: If you're referring to quick actions / link previews, you can get this with a plugin. Otherwise force is readable via events.
3. Apple Pay: There's evidently plugin for it, but I can't speak to whether it would work for you or not.
5. Size Classes are not applicable to your web code. Instead, you should build your app using responsive design techniques. This accomplishes essentially the same thing.
6. iPad Pro 9.7 is fully supported. iPad Pro 12.9 will be up-scaled as the current version of cordova-ios doesn't support generating launch storyboards yet. You can add them yourself manually, or wait until it is supported. If you want to live on the edge, try my PoC plugin: GitHub - kerrishotts/cordova-plugin-ios-launch-screen at 2.0.0 -- I'm doing this as a plugin to figure out things should work before trying to put this into the cordova-ios platform itself.
9. Cordova usually supports a new iOS release shortly after public release (no betas!), but that doesn't mean /every/ feature in that release is supported. For example, iOS 9 brought us split-screen multitasking, but PhoneGap doesn't yet easily support it (you can make it work if you want to get your hands dirty, though). Another example: share extensions can be worked into a PhoneGap app, but seems to require some native code tweaking on your part.
Hope that helps!