I just took a look at the MFN-20 test league and here is what I saw.

From 2014 through 2019 there were no 2000 yard backs. From that point on, the seasons are listed individually.

2020 - 1
2021 - 2
2022 - 1
2023 - 3
2024 - 1
2025 - 6 (From 1973 through 2013 there have only been seven 2000 yard backs in NFL history)
2026 - 3
2027 - 2
2028 - 1
2029 - 3
2030 - 2
2031 - 1
2032 - 4
2033 - 1
2034 - 2
2035 - 2
2036 - 1

For 23 seasons there are 36 2000 yard seasons.

This is a bit extreme when compared to the NFL data. I wonder if increasing penalties will help lower the number of 2000 yard backs.

Another item that I hope to roll out soon is the ability for defenses to key on the run/pass, which I hope will help pull these numbers down. I hadn't thought of penalties having an effect, but that's a good thought too.

More than penalties, I think the yards per carry is too high for certain runs in particular

The outside running plays tend to yield a lot of big runs.