You might try riding without your Clipless system for awhile and see if your knees are better.
Although most Clipless user's are convinced they have an enormous advantage I regularily beat riders using them while I have simple, comfortable MTB pedals.
I'm so accustomed to clipless pedals that I find myself yanking my feet right off the pedals if I try to ride my bike without being clipped in. It isn't the performance advantage that makes me ride my bike with clipless pedals, but instead for safety and comfort. Safety, because I ride a recumbent bicycle where my leg could get sucked under my seat should my foot slip off the pedals and hit the ground while underway. (Some folks have gotten some nasty lower leg injuries as a result of leg suck.) And comfort because I can pull on the pedals as well as push on them, keeping me from getting "hot foot" from constant pressure on the bottom of my feet. I also feel like my quads don't tire as much when using clipless pedals. But it is all what you are used to, so I'm sure there are plenty of folks that ride without any attachment to the pedals with great success.
I'm tempted to add clipless pedals to my kayak (as someone posted on another thread), but I don't know if I want to abuse my bike sandals by getting them wet all the time. (Although I could wait until I'm in the kayak before I put the sandals on... still ruminating about switching the pedals.)