This is the issue that will bring politics into the equation.
I read the article. For the fans and talking heads, the idea of a super conference is great for conversation during the off-season. However, even if 16 schools decided to form a super conference with 4 team divisions you are going to have the same structural problems that are present now - one of the divisions convincing the networks that they are superior to all others and demand more exposure (read more $$$) and play-off positions.
ND has made it clear they will stay independent in football (for obvious scheduling reasons and the NBC tie-in) so that kind of blows the argument apart. Stanford's strength is in the spring sports so how does that help a football super conference other than giving USC a team in the same time zone?
Finally, no super conference will include oSu and TTU even if not having oSu knocks out ou because of the legislation tieing ou and oSu together. (I suspect when push comes to shove ou would garner sufficient political pressure ($$$) for oSu to gracefully decline an invitation.)
If the schools want to blow things up and start all over again they first need to grow a pair and: 1) No independents eligible for the "new" CFP (call ND's bluff); 2) games against independents and lower classification teams count as losses in determining playoff positions; 3) 75% of games have to be conference games; 4) teams in each conference must face every other conference team twice in any 4 year period; and 5) limit CFP to conference champions.