Wisconsin's offense would have been better served if they had a future all-pro Super Bowl champion at the helm? Who would have ever guessed.
The point is, Nebraska provided a model for Wisconsin's improvement the last two decades, and now it can return the favor for us. Wisconsin year in and year out has a very solid rushing offense despite, with the one exception you noted, having a generally mediocre pro-style QB in there as game manager. There's no question that Wisconsin's offense could be deadly with a better QB at the helm, guys like Lee or O'Brien or Gebbia. That's what we should aspire to, and Riley is smart enough and experienced enough to build on what Wisconsin has done and make it better.
If you're looking for an example of how a team can be dominant running the ball despite having a pro-style QB, you don't even need to look outside our division -- both Iowa and Wisconsin (as well as Michigan State and Penn State in the West) follow that model, and they've made it to plenty of championship games and Rose Bowls doing so. And generally with recruiting classes that are consistent with what Nebraska does year after year.