My first change is the spiking of the ball to stop the clock late in the game. As I look at it, it meets all the criteria of intentional grounding, 1) The passer is not outside the pocket, 2) the ball does not reach the line of scrimmage, 3) no receiver has a realistic chance to catch the ball, and 4) the passer is facing imminent lost of yardage. Translation: Teams should have to manage their time outs better.
Next I would change the rule on facemask, not only for the defense, also to include the offense. As it is now, grasping the facemask of a ball carrier or QB is 5yds, but does not include the offensive player ( ball carrier) who stiff arms a defensive player in the facemask. Also on Pulling, twisting, or turing an opponent by the facemask is a 15 yd penalty plus an automatic first down. To me that's two penalties. Pick one.
How about the rule of being pushed out of bounds in the endzone. That's why players go to the corner hoping they will get pushed. Then the officials have to determine if they would have come down in bounds had they not been pushed. You should have to come down in bounds with full control of the ball, period.
No more just having to break the plain for a touchdown. Half of the players just throw the ball and don't have contact when it hits the plain. Make the player have the entire ball over the goal line and have possession. There is just too much controversy the way it is now. And we all know how long instant replay take and then they only get it right about half the time.
Change the Pro-bowl to the All-star game and play in on the mainland. Also it should be played at the half-way point of the season, not 2 weeks after the superbowl. By the time the superbow is over most people are done with football. Do away with each teams bye week and take a 3 week break in the middle.
Just for GP: all overtime games are played like in college football. That way there will be more intrigue and we can see how good a manager is when he has to decide if he should go fo it on 4 down or kick the field goal.