At least two: Emeka and Kemba should have been unequivocally NPOYs. I'm still flabbergasted that didn't happen. I still think it has a lot to do with lack of love for JC, and the fact that writers seem to always tip smaller/lesser school guys.
I think this sort of thing is a lot easier to say now than at the time. Were they the best players in the country? Yeah. But in Kemba's case specifically, he just wasn't as good as Jimmer in the regular season.
It's the same reason I have Bazz #1 on my all-time rankings and frankly I think there is some separation there between one and two. He is to this program what Tim Tebow was to Florida football - people talk about his freshman year and his senior year but forget the fact that his decision to return to the school and play at an all-American level his junior year kept the program from becoming completely untethered. I actually don't think it's close between him and Kemba and I still think Kemba had the greatest single season in program history.
Now, if people are going to make the argument that guys like Chris Smith, Donyell, Ray, etc. should be atop the list because they paved the way for everybody else, fine. But I don't think that's the way it works, otherwise George Miken would be remembered as the greatest big man of all-time and Dr. Naismith would be considered the greatest coach in basketball history. The point remains that within the context of the era in which they played, Shabazz Napier is greatest player in program history.