When I was 21 I was thrown from a horse and landed on my knees on packed clay arena surface. Was black and blue form knee to ankle for weeks. Since then I have had knee pain myself. I also have some issues with my right shoulder form a torn rotator cuff and several dislocations. Although I do have some stiffness in those areas and sometimes pain I have found that the best thing to do is keep the surrounding muscles strong.
When I was not riding a lot I would get off a horse and be almost crippled with my left knee unable to bear weight for about 10 minutes due to it locking up. If I am riding regularly or doing other exercises that use the muscles I have very little problem. I also take a joint supplement that helps a whole lot. Combination of Glucosomine and condroitin and MSM.
My current big issue is that once fully flexed I have no power to push and wind up using upper body strength to get back up. This is making it very hard on me to come forward out of the back rolls. I figure I'm doing the best I can and perhaps I'll be a long time if ever getting it down but hey I'm not that concerned about moving up through the ranks. There is more to Aikido than just the color of the belt you wear.