It would make a really big difference if RetroPie gets polished and feels more like a real console. With GUI settings and no further need of ssh-ing or editing config files.
Just some simple settings like audio and video output like OPENelec has within XBMC.
Per emulator or in general. I noticed that the 2.4.2 beta introduced something similair to this and would love to see that evolve into a fully integrated system.
Or standard hotkeys to switch between shaders. These little tweaks in the GUI would make it more user friendly.