What sort of insoles are you using? In my experience, about 90% of the insoles that come with shoes (cross trainers, runners, basketball shoes, anything) are absolutely useless as anything other than a soft surface to land on.
Go get a good pair of insoles for your shoes and see if that added support doesn't decrease the shock on your joints.
Not to plug a product here (I don't work for them or anything, this is purely recommendation out of my own satisfaction, and I feel no guilt in doing so as this is the ONLY way the company advertises, by word of mouth) but SOLE's custom heat moldable footbeds are quite amazing. I've been wearing mine for 2 years, they still look exactly like they did coming out of the box. No wear or damage, so that's always a good sign.
The actual support though is AMAZING. At first I noticed a slight feeling of forward propulsion, but after wearing the insoles every day for 3 months, no other pair of insoles gave me comfort to the same degree. With the soles, you get the arch support where you need it, and believe me, it's a good arch support (look at the pictures of the insoles, you can clearly see the arch support which your current insoles lack, if this support is too high or low, it'll mould under the weight of your foot to produce a good fit which will change over time as your foot adapts so your consistently have a strong arch support which will help mould, and maintain good form in your foot.
Please note though, nothing replaces real orthopedic inserts. Having worn orthopedics before though, I can say that these inserts will come in at a very close second. I think they even come with a satisfaction guarantee.
Check them out, it's worth a try. Your mileage may vary, but I feel quite confident in saying that you'll probably end up putting these inserts into every pair of shoes you own and will be too spoiled to settle on anything else. At least that's what ended up happening to me. I can honestly say I'm never wearing the default insoles that comes the shoes when I buy them again.
For the record, I've been using their ultra softec series.
I wont plug their URL into this post (to avoid this looking like an advertisement, in case anyone doesn't like that), but if you go on google and search up "soles insole" they should be the first result that comes up.
Read up though, you'd be surprised how many runners' problems can be attributed to bad foot support from their shoes or insoles.
Another product I've been quite happy with (having muscles in the backs of my legs that get very tired) are Thorlo's anti-fatigue socks. They're designed for security guards and law enforcement who have to spend long hours standing or walking on patrol and who often get muscle or joint problems in their legs as a result of doing this as part of their job. They work as a light tensor over the entire leg below the knee cap and have a mesh pattern that helps increase the circulation in your legs to help prevent them from getting exhausted.
Since their actual intended application is in the line of law enforcement, they've also got anti-microbial fabrics sewn in which inhibits bacteria from surviving within the sock. Originally this is designed so officers don't have to worry about infections from walking through contaminated blood. The side effect though is that you can wear a single pair of socks every day for over a week, including during your workouts, and they will never smell so bad that it becomes offensive. I don't advise this, just cause it's gross, but it does mean you'll never have to worry about how bad your shoes and feet will smell after a run.
They're originally designed to be worn in a 4-6" high-cut boot, which the user will be running in, so they're made with a double cushioned (not double-layered like many specific anti-blister socks) stitching to prevent blisters. They do this job well in a pair of boots, but in shoes, I don't think blisters are even possible unless you specifically try to develop them.
I've actually had to stop wearing these socks during my workouts because my lower legs weren't really feeling the workout at all. However, this may benefit you.