In most of the scenes that involve the aircraft but particularily the fly right by scene when pilots are flying wouldn't they pull the thrusters back towards them in order to go up and not down as they actually do
I think you might have this wrong but I'll check again to make sure. If I what you are talking about is when the MiG 28 goes by, Maverick did it right. The thrusters as you put it go forward in a plane to slow it down. What he pulled back was the lifter.
NO NO NO, you have it all wrong. Maverick can't get away from the aggressor A-4, so he has the plane pass him. He cuts the throttle (not thrusters), deploys the speedbrake, and pulls back on the stick. This causes him his plane to loose alot of speed in a very short time. When the A-4 flies by, he then goes to full military power (everything short of afterburners), dumps the nose to pick up speed and is now on the offensive, not the defensive.
When I first saw the maneuver, I thought "Not a good idea, Maverick." I've only flown against F-14s once, and they tend to telegraph their energy state with their wing sweep. Forward sweep,and they're out of energy. To go to idle, pop the boards, and pull full aft stick will cause an overshoot against a reasonably stupid, non-proficient aviator. Against an aircraft with above-average low-speed handling characteristics, such as an A-4, it gets you gunned into next week.
All of you who say that this maneuver is stupid don't know too much about military history. Randy Cunningham and Willie Driscoll, the Navy's only Vietnam Fighter Aces used this exact same maneuver on one of the top fighter pilots in the Vietnamese Air Force, who was flying a MIG-17, even more maneuverable than an A-4. This is a move that has been sanctioned by the Navy as very effective. The point about the F-14 giving this away is valid, but the F-14 pilot can manually control the sweep of the wings if he so desires, and would be able to fool a pursuing aircraft.