I had a motorcycle accident 2016. Operation on both knees after PT did not help in 2017. I have tried mtb style, road bike style and then I tried speed play pedals. Speed play with the extra float was easiest on my knees but still hurt on longer rides.
I use 510 pro flat pedal shoes and flat pedals bigger at least 100 x 100. The smaller pedal I tend to get host spots on my feet.
If you really must clip in instead of flat pedals I would look into speed play pedals after you have dial in your fit ( seat height, bike frame, crank length etc.. )