I've just uploaded a video to Youtube which describes the method used to allow NES controllers of all types to be utilized on Atari systems:

https://www.youtube.com/watch?v=yKloEnCYTwI

I want to credit AtariAge member, 0078265317, who was the smart guy who discovered it.

Also presented in the video is the PC gameport controller adapter for the Atari 5200 which has allowed me to play numerous games with a Saturn-like controller as well as a Gravis Gamepad Pro which is identical to the original Playstation 1 controller... and something no one else knew before about getting Atari 2600, 7800, and Master System controllers working on the A5200 for a reasonable price.

Enjoy!