From my personal (and limited) experience i can say, that the PhoneGap Build seems to actually be better than CocoonJS.
- PhoneGap Build supports Android 2.2, while you (apparently) need at least 2.3 to be able to use CocoonJS - although this means that only 5% will be left out, i am a part of these 5%, therefore i feel that this should be mentioned (as i said, my subjective opinion). tbh, i simply couldn't get the CocoonJS exported app to work even in an emulated Android 2.3 (used VirtualBox, everything else was functional), i personally found this to be frustrating
- PhoneGap Build has an easier and simpler interface, no launchers you have to search for on Play Store, just go on the website, upload your .zip file and build a project, download the .apk file (or whatever you are trying to build the app for), install and you're done, you won't have to wait for e-mails from ludei, because the app build process literally takes seconds
- furthermore, you can upload things from both public and private GitHub repositories, so you should be able to easily work together with your friends, and while the free version only supports 1 private project, there is nothing keeping you from using it for exporting and building, and keeping the .zip files stashed away on your HDD somewhere
- also, the file sizes differ greatly, a project that was 10MB when exported from CocoonJS, was just 1MB from PhoneGap (the actual project .zip was around 500KB)
While both are free, i found the PhoneGap to be much more pleasant to use, of course, you guys can feel free to disagree with me. :)