I got my controllers working on my retro pie. I just had to press random keys on the keyboard until I found one that opened the controller config. From there, I was able to just press a button on each controller and have it recognize them. It allowed me to match up the buttons with the configured buttons, and then worked as expected.
My controllers aren’t that great. I have a Logitech Precision (like a Playstation 1 controller) and a Nyko Airflow Ex (like a Playstation 2 controller). Testing on Super Mario Bros., the Logitech was decent, but I wasn’t able to maneuver as quickly and easily as with the regular NES controller. I struggled significantly more with the Nyko.
Both my controllers should handle some less demanding games just fine or passably, like RPG’s and overhead adventure games, but I think I will want to get something better. My cousin used PS3 controllers, which connect via bluetooth. They were pretty nice, except the joystick seemed hard to control in Mario Kart 64. I may go for one of those or look for a computer one with good reviews for old console play.