I agree, the current approach of using the REST API to develop the data layer that's backing a user interface seems a bit unconventional. The big advantage it brings though is that in the case of PhoneGap, the app can be developed on a desktop browser first by sending requests to the Listener or the LiteServ utility app; making the "write code, run it" cycle a lot faster than deploying it to an emulator on every change. To achieve that with plugins, PhoneGap has a proxy API in which functionality can be stubbed so that when it runs on a desktop browser it won't fail (since the stubs replace the calls into the native API). So it should be possible to have the same ease of development with a PhoneGap plugin as with the REST API.
Regarding the development of a PhoneGap plugin, I don't think that a direct JavaScript binding for Couchbase Lite would be usable in the case of PhoneGap because it runs in the (mobile) browser. It would be usable for other frameworks like React Native (maybe NativeScript as well but I'm not sure). In other words, framework plugins are on a case by case basis.
For remote access to the database, it does make total sense to have a REST API but only for remote access. I think it's important to keep in mind the difference between the two use cases (app development vs. remote access). And if the REST API is indeed an adequate solution for remote access, to build out only the features that satisfy that use case (i.e 100% parity with the native API may not be needed in this case).
James