If you're going to have the remap menu there you should at least make it work.
I paired up the PS3 controller and wanted to use it with FPSE since the key layout matches the PS1, but I couldn't remap start and select for it plus it didn't even seem to recognize the right analog stick.
The key remap is one of the biggest issues for me. Either make sure it works (including saving), or remove it and include a map overview instead, as well as a selection of profiles depending on what controller is connected. OUYA supports a range of gamepads, including PS3 and Xbox360, people will want to use at least those three types.
Beyond that I fully appreciate the effort to bring the emulator to OUYA and have sent you some dollars through the store