"My profession does require more of my body than most people however, very few professional athletes have issues like this as they get proper treatment. It is the standard of the treatment that concerns me. I am a helicopter winchman so spend a lot of time squatting. After a fall of ten feet and damaging my ankles my knees started hurting quite badly after i was able to walk again (after 3 months). I suspect my knee issues have came about from the mismanagement of my ankle injuries as i only received half a dozen physio sessions (again it comes down to money, there is one physio for a LOT of people.) After my session with the podiatrist he identified several issues from my gait. He thinks it is highly likely that my injury has caused all my problems as i never had any issues before then. Covering the issue of "state of cartilage and joint surfaces;" is half the issue i have, I have not had a single test to find out the state of my knees. All i seem to get is lines drawn on my knees and my muscles measured.
I shall be getting my orthotics shortly so hopefully this will fix things and i can completely bypass any physio. "

Aha, now there's a bit more to be going on. How severe were your ankle injuries? fractures? What was doing during these 3 months befoe you walked again? in plaster? I'm not in the UK any more but I do agree that top atheletes get top medical care from the initial treatment and surgery to physio as they are in a moneyd industry. They do here. But if say a top athelete fell 10 feet and broke his ankles he might not be a top athelete any more. He'd probably have enough money for changing his career...... I do not envy your situation. I'm sure the physio also attributes your problems to the after effects of the accident. He probably wasn't involved in initial diagnosis and treament, or was he? (immediate post accident?)
Exercises can be to mobilize or strengthen or to put optimize/correct the movement dysbalance that has occurred due to accident or disease. There are sometimes limits of effectiveness due to nature of the problem (joint surfaces damaged, inflammatory conditions...) or the impossibility of the person to do adequate training or the wrong demands on the damaged joints at work. Have you had/ needed manual mobilising of ankle joints and knees to reach as much normal range of movement as possible? Is your knee and foot movement as pre-accident?
It can be that strengthening exercises and increased muscle bulk aren't the only or optimal way to go but I can't assess you online.
I would refer you back to the doctor and if necc get a second doctors opinion and not let go till I got it. Let the physio off the hook a bit. He is not a car mechanic and can't repair you as such. Try and get him as an ally to approach the doctor together. My opinion is the army owes it to you to help. X rays of knees aren't that expensive.
I've no idea how the army treats employees who are unable to do their original work, that,s your job to find out and maybe, if all else and your knees and feet fail, consider retraining. I suspect that it's not going to be easy. Downgrading doesn't sound fun.
Keep us informed!
regards Jm