Lennon took what Thomas built and took us all the way to the top. Thomas had to clean up the mess Pat Behrns left behind. Thus the difference.
I will argue that the athletic department did not give Lennon the resources needed to be great year in and year out. If they had, we might have become what GVSU became during the 2000's (not to open up old wounds, but it's true). Now we have an administration that is committed to putting the necessary resources into the program (IPF, FCOA, etc.) to make it a perennial FCS power. It is just too bad that the athletic department was in chaos when Lennon left for SIU and we promoted Mussman from within. We are still paying for that right now.
In basketball, you can have one player change the program overnight. Football is more of a numbers game and requires a lot more time to build a program into what you want it to be. NDSU did a good job building their program during their transition (their 3-8 year in 2009 notwithstanding) so that when they were playoff eligible, the program was ready to take off. UND meanwhile spent most of the transition losing to USF and getting blown out by established FCS programs.
These aren't excuses, they are facts. And facts tend to be stubborn things. It is way too early to talk regime change.