If I understand your question correctly, you want to be able to use push notifications (and the registration token is for that).
I haven't used it myself (yet) but phonegap push plugin recently (see announcement from August) moved to work through FCM.
The old plugin used to work with GCM and now they migrated it to work with FCM. It supports both Android and iOS and still, if you want, let you use APNS as older plugins used to do.
The project seems to be better documented, with lots of example payloads, detailed options and nuances of each device etc, and is very active (108/1544 watches/stars vs. 58/418, on 2017-11-04) with latest update a few days ago (vs. 5/6 month for cordova-plugin-fcm).
From my impression, phonegap-plugin-push is more widely used...
With that being said, I don't have concrete experience with either - only with the predecessor of phonegap-plugin-push.