Honestly, you should take a look at Roughing the Passer.
It looks silly sometimes, but when set to 54 or 55 in Madden 09 through 12 [so I assume the same for 13,] roughing the passer is the best way to replicate defensive penalties. You will see a defender and a QB after the throw slow to a walk and the defender will touch the QB by accident and the QB will go flying and the flag will be thrown. You just have to accept that as a simulation of a defensive foul. Pretend it was a PI or something else. I hate it, but that's the best way to get a correct number of flags/yards per game.
It also helps give the AI [and the user] free first downs just like in real life that keep drives alive.
I tend to use these penalty settings:
False Start at 0 & Off-sides at 100. I know false start at 0 isn't that realistic, but it's the better of two evils in my opinion. You see, for years in Madden, the AI will line up for a FG and use the cadence and get a false start to back them up out of FG range and punt. The computer putting up 3 points instead of punting makes a big difference, so I'll live with 0 false start. Also, I rarely saw my defenders ever jump offsides. Even with false start at 5 [I never tried 1, and I might just for the heck of it] the offense would "jump"
far more often than the D line. Also ,at 5, I still saw a LOT of field goal attempts get pushed back. The AI LOVES to use the cadence on FG tries.
Holding, clipping, face mask all at 54. 55 makes these flags come in all the time, just like with roughing.
They rest don't appear to matter at all. I have them set to 100 and never see them called.
Penalties per game
Penalty yards per game
Going back to 2003, teams average a low of about 4 per game to a high of about 8 per game. Most teams commit 5 or 6 a game. Teams also average anywhere from 35 yards to 85 yards a game. Most teams fall in the 50 yard mark. That makes sense given the average of about 5 or 6 a game. If you see about 5 or 6 a game for about 50 yards a game, along with about 120 to 130 plays per game, you are right where you want to be.