I think that both Barry Switzer and--even more so--Urban Meyer are being punished for some unwritten "morality clause" in the criteria.
Conversely, I think Bob Stoops is getting some bonus points for being a stand-up guy.
I do not like Nick Saban, but he should be #1. His championships are all legit, earned through the BCS or CFP system, even though two of them came after he didn't win his division in the SEC. Bear Bryant's championships are from a different era (as are those of Wilkinson, McKay, Parseghian, et. al.), where until 1968 (AP) and 1973 (UPI/Coaches) named their national champs before the bowl games, and there were often split championships. Going back further, national championships earned before the AP Poll appeared in 1938 are even shakier.