Sixteen?! Your Spider-Man's such a baby! I promise he's much older where I'm from. Still might want to avoid the situation if you believe the scuttlebutt. Never been to partial to that kind thing myself. But that's a conversation for another time.
S.H.I.E.L.D. and the military still doesn't always play well together, but there are a few of us out there with eyes good enough to see the big picture. It helps when you're a member of the Avengers as well as several other intergalatic organizations. You'll have to catch me up on the differences over that coffee Coulson.