@skullmonkey It's already done and in version 0.81
I called it BashROMManager

It does not support subdirectories but let us select ROMs folder for each system.
Feel free to test and report bugs into the thread.

@MarcB it's the global RetroArch config file. But some configs are in other files.
For fast-forward for example, the input_hold_fast_forward_btn = "7" line
in configs\all\retroarch-joypads\Xbox360WirelessReceiver.cfg is enough. But keep in mind that this config will work only for your xbox joypad.