The danger of not thinking things through

I've often said my issue with going to a playoff system in college football is that people are so eager for playoffs, a good plan is yet to have bee presented. I will admit that even the Victoria Times solution, reorganization into 12 conference tournaments with the champions of said conferences entering a 12 team conference. It addresses some things that I have an issue with in most plans: It gives everyone a chance, makes the regular season matter for every team and does away with any influence of the polls or media. The problem, of course, is that teams like, say, Colorado wouldn't go for it, now that they are in the Pac-12. They have a stated desire to play on the west coast, where recruiting is plentiful. In our geographic realignment, they would play schools essentially in the middle of nowhere.
All that said, this piece by Sam Eifling is also met by logistical oversight. He makes the argument FOR moving to the 4 superconferences that many have stated they expect to see coming by showing the cupcake games some teams have played this year so far. I have two issues with his piece:
1) Eifling's examples include 6 non FBS schools, which takes away from his "BCS conference schools are better" argument. Of course those schools are worse. They aren't even at the same level.
2) He fails to note that the real issue is that, of the FBS schools refuse to schedule the GOOD non BCS schools. He introduces matchups like Oregon vs LSU, but he doesn't point out that nobody wants to play a school like Houston, for fear they might get beaten by an up and comer.
I understand the allure to playoff enthusiasts of the idea of super conferences. I worry that we will never see a school remake it's reputation as a football powerhouse like Utah, TCU or Boise State ever again. Teams like Houston and Boise State will be left the cupcakes in the NCAA, and be forced to play them across their entire schedule. Good football schools will be forced to become cupcakes too.