I really don't think that playing flag football once or twice a week did anything for me in the way of physical conditioning. Gym should be more of an exercise class and less about sports. Kids who want to play sports can try out for the school team.
I'm on the fence regarding P.E. being a requirement. My reasons are lengthy and eccentric, so I'll skip them.
FWIW, I have two teenagers who play a LOT of video games. Elder-Son is 5'8" and 135 lbs. Younger-Son is 5'6" and 110 lbs. The younger one has been into jiu jitsu and swing dancing lately...he's pretty active. The older one is a couch potato. I don't believe that being sedentary makes you fat. Consuming too many calories makes you fat. People tend to consume too many calories because they eat highly-processed diets, believe that "fat-free" means "eat-the-whole-bag", and don't eat enough fresh fruits and vegetables (which fill you up and make you want to eat less, overall). It's lousy nutrition that makes Americans fat.