I currently ride XC on flats, unfortunately I have been experiencing swelling and minor pain in my knees as of late. I've visited a sports therapist, he said my outer quads aren't as developed as my inner ones. (sorry for bad medical wording/knowledge). I find that I have half of my foot off the pedal while biking, putting power through my big toe. If I were to switch to clipless pedals would it force me to use my outer quads more? Potentially correct the imbalance? I have been doing the physio and have been focusing on putting power through my pinky toes instead of my big toes. I'm not sure if this is proper. Any advice or suggestions would be lovely, thanks.
Unfortunately changing your pedals will not fix your problem. Mountain Bikers like many athletes develop muscular imbalances through poor movement patterns and repetitive use. Switching your pedals to avoid knee pain will most likely only further your current muscular imbalance, promote increased compensation and eventually additional overuse injuries. Without a thorough evaluation it's hard to say, however the knee pain your describing is an issue I see everyday when treating both athletes and non athletes in physical therapy, and more than likely a combination of both poor alignment and muscular imbalances at your hip and ankle. Correcting both posture and poor movement patterns is your best bet initially. Also, our big toe's are designed to facilitate 'push off ' during normal walking and running. I can offer some more advice/instruction if needed that might be able to help correct some of the imbalances your referring too. I recently posted a video on youtube/Facebook entitled 'How to Identify your mountain biking muscular weaknesses' that might be helpful.
Is it possible that your saddle is too high? I had a similar problem, but this was fixed after a bike fit. The biggest change in the bike fit was that my saddle was lowered by over an inch (I thought it was good before that!). Now I see a lot of people with the same problem.