The offense wasn't the problem against Wisconsin. It was special teams, and the fact that our defense couldn't get Wisconsin's offense off the field.
Typically, while it seems that we run the ball alot, we usually seem to be roughly 50/50 or so in terms of run/pass. I seem to remember in last year's game that we didn't really start scoring points and take control of last year's game until we started throwing the ball more in the 2nd half.. We were running the ball on almost every down in the first half last year, and the result was a 10-3 halftime deficit.
I don't see the fact that we threw the ball more this year against Wisconsin compared to last year as a problem, and certainly doesn't point to why we won last year's game, but lost this year. We were still moving the ball and scoring points. If it was working, why not continue to throw the ball? As Hayden used to say, scratch where it itches.
Two times when it really mattered the defense did their job and got Wisky's offense off the field. However, one of those times the punt return team let them come right back on by not being disciplined and allowing the punter to run right up the middle.