I haven't done a thorough statistical analysis to definitively prove this notion, but I'm almost certain from observation that the number of first downs gained through penalty is way, way below what it should be. I think in an average NFL game u can expect at least 2-3 per game, and I'm almost never seeing any.
I'm definitely sure the number of overall first downs is noticeably low. However, offensive yardage, which I have done a complete stat analysis of, is being gained at a very realstic level.
Therefore, the obvious conclusion we're ;eft with when taking these two factors together is very likely that not nearly enough first downs by penalty are occurring. Bump up this AI setting or whatever it is, and more first downs will happen, then more points will be scored(points scored is def low, noticeable enough to not require a thorough stat breakdown).
I see the expected number of penalties overall, but a noticeably inordinate number of, for ex, resulting 3rd and 5's, rather than "automatic first downs", which I can hardly remember seeing at all.
So, even though the overall number of penalties occurring feels right, it is the type of penalties being called that is not reflective of a real pro football gane and needs to be adjusted for more optimal results.

It's not really a bug, but it is something we've never looked at. The penalties.xml file is where these items are, but you're right, there isn't anything in the code that sets a "weight" to the particular penalties. If you have some data somewhere that I can go on I can look at adding and weighting the penalties correctly.

A related side question, and I can make this its own thread if you prefer -

is the game coded with roughing the passer penalties? Obviously, esp in today's game, this is one of the most common and most impacting penalties we see in the NFL. I am pretty sure I've yet to see one called here. Can we either get that added, or do what we can if possible to have it called closer to the number of times it is in real modern pro football games? Again, and I could be way off, but this one strikes me as another desirable feature in terms of "Bang for buck", as my educated guess as to the ratio of amount of effort it would take to throw it in vs how much "realistic feel" it adds to the game is that it scores quite high in that regards (as opposed to, i dunno, "hey can we get horse collars called in our game?!", assuming that isnt already called, as something like that is on the other end of the spectrum - any extra little detail is nice, but nobody but the most ravenously OCD of fans is gonna miss seeing horse collars specifically called, and those types of little bows ons top are nice when everything else is already implemented and running smoothly, so for us maybe by 2030 ;-)

Once of our power users found some stats so I'll be able to make the penalties more realistic in the next version. In the meantime feel free to mod the Penalties.xml file if you want to add some different penalties. In theory adding the same penalty more than once would give it a larger chance of occurring... I haven't tried it and it may break, but if it works then it may be something worthwhile to you.