It is my personal view, and i am not an expert either.
If you have much fat (boso) in your thigh, i think you can either go for surgery or exercise in Gym. Thigh exercise will burn your fat but you may see some muscle also.
As you already mentioned, you play sport a lot, running should help you to cut off some fat. As far i know, runners do not have big muscle but strong leg/thigh.
I recommend you to hike in uphill or run in treadmill with some incline. Run until you can not walk.

(If follwoing my idea is tough or problematic to your health, stop it and seek different way out.)
good luck

 

As far as flexibility and stability, problem might be with your ankle and calf. Try calf/ankle stretches. Do you ever get shin splints?

@ stiffler
I got shin splints problems. When i was kid i used to be a vivid runner. Back theb did not have any issues whatsoever. Last year i picked up running and suddenly i started to feel the pain. FYI i got flat feet. Do you have any suggestions? Any help is greatly appreciated.

That’s what I thought. I believe it is more aptly called medial tibial stress syndrome.

The good news is that there are some ankle stretches that you can do to strengthen the lower part of your legs. I had the same problem and now I have been able to control my splints to a very good level. When done routinely this will also help restore the flexibility and strength; however don’t ever do it wrong, you could cause more damage since ankle joint is a fragile part of your body.

Here is a link for you which talks about shin splints and exercises. If you don’t know what few terms (such as dorsiflex and plantar flex, google or youtube search them).
http://www.sportsinjurybulletin.com/archive/0161-shin-splints-treatment.htm

 @Inflexible: If you ask me one exercise that would help in Lower Body Flexibility that would be SQUATS!! regular or with help of weights, this will help you strengthen your lower body as well as make it flexible.

@baalai and Stiffler : I have been a avid runner myself, the recommendation I am going to give you might shock you as this goes beyond the normal norm. To run injury free go BAREFOOT!! I would let this video do the explanation or look at this websitebarefootrunners.org/build2/ !! If you need further info let me know, I am barefoot/minimalist shoe runner myself (just started 2 months back)!! May be in a Year time i'll run Marathon Barefoot :-))

 Still Interested??

Then Look at this Video!