You have several ways to improve this ability. For each 17 expired meters your endurance is increased by 1%. Same as for each minute cycling or swimming. You take part in a triathlon, it vastly improves the value.
It improves the value of "Shooting", you increase the values of accuracy, Ammo capacity, loading speed and Crosshair behavior. You can improve the skills by eliminating opponents, shooting on the head, or if you completed challenges on the shooting range.
You can increase your melee damage, and at the same time reduce the damage you take. With 20 strikes the value is increased by 1%. But you can also do sports like tennis or golf to gain more power.
The higher the value of the crawl, the lower is your sound radius. It also enables to make you faster and quieter movement. For each 45 meters that you sneak, improves the ability to 1%.
To have more control over your car in the air, you must for example do a wheelie or perform many jumps with your vehicle for each 10 seconds. The value is increased respectively by 1%. You however receive the biggest bonus, if you land at a monster stunt on all four wheels.
Every minute that you remain under water, increases the value of your lung volume by 1%
The higher the value of flying, the lesser it is to have turbulences during the flight. Also, it facilitates start-up and handling.