There were some powerful independents back then, which in included not only GA Southern, but team like Boise State, Central Florida, Hofstra, Liberty, Troy State, Western Kentucky, Youngstown State and several more (I guess my mind is going). In fact, GaS and YSU won the majority of their titles as independents. At that point it was much easier to get an game outside of your own conference and not play someone from another conference. I have never liked the idea of playing up or down, as PAllen said, you never know. If you only play I-AA/FCS teams, then you have a better idea of how good someone is. Also if no one is playing money games, then we do not have to worry about financial superiority of some clubs.
I will further state that if the NCAA does not take equal post-season representation from ALL conferences, then there will be an unfair shift in the recruiting base, which basically means that a bad team and/or conference will always be just that.