They've said that it has actually been a really close battle for the starting QB job. Not sure how accurate that is, but to me it looked like O'Brien was handcuffed by the play calling, or that O'Brien was/is afraid to audible for fear that if he audibles and makes a mistake it will be back to the bench with him.

Let's go back in time to 2003. UW vs. #3 Ohio State. Starter Jim Sorgi gets knocked out of the game, and backup Matt Schabert comes in. UW is deep in their own territory so OSU is thinking the Badgers will be conservative with a backup QB in the game. Lee Evans runs a safe short stop/slant route and the OSU CB tries to jump the route... only they pump fake the safe quick throw and Evans runs a go route and Shabert hits Evans over the top for a 79 yard game winning score. Similar situation here - starter gets knocked out, but does UW try to outsmart the defense that is keying on the obvious (handoffs to Ball)? No, they go conservative. You can't shut down the playbook when your backup QB comes in.

Maybe the conservative play calling is a result of lack of confidence in O'Brien, but I don't think whether or not they run the fly sweep (which they didn't run once the first three games of the year) has anything to do with who the QB is.

The Badgers, IIRC, ran one reverse/"fly sweep" against MSU, but ran one on the first play against Indiana, three in the first quarter alone, and by my estimates at least 10 during the entire game today. While Indiana's defense is not what MSU's is, I don't think it is any coincidence that the more they run that play the more it opens up the running game for them. The change in QB wasn't the reason they put up 62 today. The Badgers open up the playbook against lesser teams, but against the better teams they get tight and conservative, and that's what has cost them.