I would suggest that making the defenders actually play the ball and react to the pass, as well as taking away the unrealistic scramble-passes would probably drop the completion rate down. I dont think the passing game should incur an arbitrary penalty, since just removing most of the unrealistic plays would drop completion way down.
There should never be a single completion on a lob ball into triple coverage, thats a couple of completions removed right there. Lob ***** into double coverage should be way, way less effective. Also, like people already said, the scrambling throws to the opposite side of the field while running should either not happen or happen only for dumb qb's and result in incompletions.
I subscribe to the thinking that, if you strive for realism, most of these problems take care of themselves. Giving a, arbitrary penalty on throwing a lot is not realistic. Taking away the unrealistic throws and giving DB's better chance to defend a pass would do exactly the same thing.
Just my 2c. Still thinking about whether to purchase more time with the game. I really understand how hard building something like this game is, but i'd love to see a goal of realistic play instead of bandaid fixes to get realistic stats.