I certainly agree that KSU needs to give Prince a couple more years to get his players in here. However, if I were a KSU fan, two things would really worry me. First, Prince's teams seem to play with a lack of discipline. This has nothing to do with talent. It has to do with what a coach demands of a team. K-State is a highly penalized team and the defensive players seem not to be assignment sound. Even when Prince gets his players in here, assuming their more talented, if they play with the same lack of discipline, KSU will struggle.
The other thing is strategic decisions. Like focusing recruiting on skill players and developing linemen in the weight room. I believe the quote was that you build a team from the outside in. I would be worried if that accurately reflects his recruiting philosophy. Also using a 3-4 when clearly you did not have the personnel for it. It seemed from an offensive standpoint, he adjusted the scheme to a poor offensive line by having a quick strike pass heavy offense. Then on defense he seems to place scheme over players.
He's a young coach, so you have to expect some mistakes and he'll probably get better. But these would be the things that would bother me.