Lower Run Block.
Also, lower Run Defense so your team doesn't dominate against the run like crazy on Heisman mode. Also, raise Run Ability...this will help, especially against option teams so option teams PLAY like option teams. On Heisman, I have my CPU at like 90 Run Ability, but like 35 Run Block and 50 Run Defense. HUM is at like 65 Run Ability, 35 Run Block, and 35 Run Defense.
With Run Block lowered, they won't pancake you on returns...they just bump you off your line.
That, so far, has improved the CPU run game, especially the option, drastically. However, not at the expense of killer kick returns and touchdowns, which is down to normal for me.