Thanks for posting on this andrew. The OLB Flat Zone defense has a couple of unfair advantages and is the reason that it will usually put up an average of 3 yards or less.
One of the advantages you will notice when scouting a team that has it active. Even if you have clicked on it during scouting several times before, it will show a 0 familiarity.
Another advantage is that there is no overuse penalty on it, you can use it for every defensive play in a game and you will not get an overuse penalty.
Dont know how that happened in current game version and coding, JDB is aware of it but I have not noticed a fix of any kind as yet.
The Goaline offense, FB Dive gains 2 yds over 90% of the time, making it almost a sure thing on 4th and 1, which is not the case in RL NFL. The only chance you have to stop it is by modifying your GL defense with two overides, and use the Attack 2 (which Ive found the best so far) by rule.
Another "exploit" that will be eliminated is on KO return, where you must use a RB, WR, or DB for KO returns. That will counter using a heavy TE with 100 break tackle and ball carry, and a "non-simulation" part of the game.