iOS 9 introduced support for Universal Links (https://developer.apple.com/library/ios/documentation/General/Conceptual/AppSearch/UniversalLinks.html) – essentially, the ability to launch an app directly given an http/https URL without requiring a custom URL scheme.
It would be nice to have built-in support for this in the cordova-ios template, similar to how the existing openURL functionality works.
I created a gist that has an implementation of the necessary delegate to do this, and it works using the existing CDVHandleOpenURL private plugin. In addition to the gist, a new entitlement needs to be added to the project (not sure if this is currently supported in a standard way), and a server-side configuration file must be uploaded to your domain.
I've tested this briefly by modifying my project in Xcode, and it seems to work well!