From what I saw, it's both. Minnesota's run game was completely non-existent as not only did their RB look like a gigantic drop-off from Ibrahim, but their run protection was awful as well as their new interior linemen struggled. As for Fleck's time management, it was pretty awful with several head-scratching time management decisions that all happened to work out due to Nebraska Nebraskaing themselves.
And speaking of Nebraska, Sims was very good at running the option and it was very effective against Minnesota the whole game. They never stopped it. The whole game. And every time Nebraska ran it they'd get at least an automatic 4 yds. Meanwhile, when you've let Sims throw the ball, a good 50% of the time it's an unmitigated disaster. So why up by a touchdown with 7minutes left in the game do you decide to almost exclusively rely on your noodle armed quarterback instead of sticking with what has worked all game long? Just blows my mind.