As a retro gamer, I have tons of controllers with almost as many unique interfaces between them, sometimes even with the same connection! So, my suggestion is this: the ultimate DB9 port controller/joystick, switchable for use on Colecovision, Intellivision, SMS, Genesis, Atari 2600/7800, and possibly even one or more of the ZX Spectrum's controller modes. Atari 2600 and SMS support should, in theory, give you MSX and Commodore as well, but those might be worth considering too.
How awesome would something like this be? One gamepad to rule them all!
I can see several ways you could consider doing this, from a mechanical slider that simply redirected control wirings to match what was needed to a microcontroller that handled the redirection of signals for you. The layout of the actual gamepad would probably be the hardest part, though going for something resembling an old Neo Geo arcade stick with a numpad added to the middle might be the best solution (and give plenty of room to work with.)
Something like this wouldn't be cheap to create, or to buy, but in a retro market where controllers and joysticks that function well are getting harder and harder to find in the wild, a single universal solution would be an incredibly welcome option to have, and even at a relatively high price point could pay for itself quite quickly. I've seen simpler versions of this, based on the 1-button layout, before, but having the full range of functions for all applicable consoles in one (relatively) convenient form factor would be swell.
Bonus points if you can throw in a functional driving controller/paddle option.