Sorry I didn’t see your post until after I posted my last one.
I am just using my pi for NES, nothing else. And I am mounting it in my dead NES with the goal of having it look and behave as close to an actual NES as possible.
As for your questions I’m not sure. Yes there is the nostalgia factor with using actual NES controller for a NES game, but the SNES also has all the buttons the NES would need. If I were to use my pi for NES and SNES I would just use the SNES controllers all the time (they are more comfortable after all).
According to the readme for the gamecon up to four controllers of mixed types can be used, so two NES and two SNES could be connected at all times and you can use either depending on what you are playing.
If I were building a multi platform emulator I would probably use PS3 controllers for everything but the N64 (I’m talking anything pre-Xbox or PS3), just because the N64 is a bit of a weird one. Also using PS3 would have sidestepped all of the headaches I just had trying to get this NES controller to work.