Alum in AZ
This is a very non-biased analytical approach to looking at this and it is very interesting and lines up with a lot of conventional thinking.
I am not even sure how you would quantify this, but most blue bloods have an era of dominance. When looking at it from a macro across eras, I feel that era can be made to look less significant that what it should be in the grand scheme of things. A key example of this is KSU. They were complete garbage before Bill Snyder came, and in his 17-20 years they were a power football program. A few of those years, they had some of the best teams in the country. Not only were they a dominate force, but this in the height of the Big 12 dominance.
This comes into context when you see a team like Boise State ranked above them. Boise State, I assume, is boosted above them largely by total wins over the eras when KSU was garbage. BSU had the luxury of playing a pretty much mid-major teams over those years and was not going up against the Nebraska's, OU's, later Texas' every year. BSU had a few nice years but nothing compared to what KSU was able to accomplish.
So I just think when you are dominate for an era it should hold more weight, than looking only at it as part of a collective. I don't know if that makes since or how you would quantify that, but its just how I see it.