With this in mind do you plan on offering a path for migration from existing Cordova apps?
Once all your plugins are supported in one way or another (Capacitor plugin or compat for Cordova plugin) you should just be able to install Capacitor in your project and see if it all works. Required code modifications in your app should be limited to the interaction with native.
Once we integrate it into the Ionic CLI, you won't really have to think about which part is Ionic UI and which part is Capacitor.