I agree his legacy will be tainted by the way football looks at the end of his tenure (assuming it has not rebounded by the time he retires.) However, he hired Joe Tiller (all time leader in Purdue football wins) and Matt Painter. He hired women's basketball coaches that have won a national championship and been to other finals and final fours.
As for Olympic sports, I think many are too quick to dismiss these projects as wasted money. At the time of his hire, the baseball, softball, swimming, soccer, and golf facilities were in worse shape than many high schools used at the time. They are now all near the top of the Big Ten. Are these revenue driving sports? No. But I can say honestly that when I was a student in the early '90s, it was embarrassing to look at these facilities. My high school of 800 students had a MUCH better baseball field and comparable tennis courts to what Purdue offered in 1991.
He may be late in doing things, but he has been fiscally responsible at every step while achieving quite a bit. I would think in today's climate of escalating debt by every level of government, that we would appreciate this a bit more.