If you are giving RetroPie a try, I have been developing an experimental RetroPie module for installing RetroFE. My goal is configure it to use the standard RetroPie filesystem layout, config settings, and use of the runcommand.sh script for launching. It should be a full replacement or complementary install to EmulationStation. I'd be happy to share it later this weekend if you would like to try it out.
My only challenge is that I don't have access to my RPi3 right now, so I am developing against the x86/Ubuntu/X11 flavor of RetroPie. There could be some minor differences that I can't test yet. However, if you could just confirm the exact list of package dependencies for installing RetroFE on RetroPie, that should be enough to get things up and running. I know that the package list used in the compilation instructions isn't correct - several SDL libraries need an extra "-0" tacked on the end for the x86 version, and I believe change are needed for the Pi too.