First and foremost, ride what is comfortable. The longer shorts do have a purpose for some riders - they offer more compression for the upper legs. Also my shorter shorts tend to rub against the seat more and irritate that area of my leg. I try to alternate short length based on the length of the ride so my upper leg is in various shades of tan - I call it the neopolitan ice cream look. I found knowing my cadence to be incredibly helpful with my riding. I was spending too much time in my harder gears and was having knee issues. Now I make sure that I spin more - my knees are happier and my overall performance has improved. The one thing I have learned in the almost two years since I started riding - everyone is different and that as long as you are comfortable and enjoying your ride, do what works for you.