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I made Number Knight using both Phonegap Build and Cordova CLI, so I can give a little insight on this.
I started out using Phonegap because of how simple it was. Simply zip your production files with a config file and upload it, and it spits out an apk. Simple. There are filesize limitations on phonegap for the free version, so that was a no-go for me when my game ballooned to over 100mb with all the added music and sound fx. I also had some problems with plugin support not being very good, so I decided to spend some time learning Cordova. It's really not that hard to use, but it takes forever to get everything installed. Java SDK's, PATHS, Android SDKS, then more Android downloads, and tinkering, but once I got it working it was pretty simple.
If all you need is a super basic hybrid app that you can get working right away, then go with Phonegap Build, and it'll work great. If you want some of the fancier features of native Android apps, then spend some time with Cordova. The extra work will be worth it once you get used to how the process works.