I split the country in half as best as possible with AFC being on the East side and NFC being on the west side. Then I just named them the same as they are now but actually used locations to determine divisions. So, the east is relatively east compared to the rest of that conference. Everyone in each division is as close as possible to the rest of the teams in their division. NFC South and North is a bit spread out but can't be helped given the location of the teams.
Geographically, it makes a lot more sense than how it is done now. For example, why is Indy in the South? We are hardly in the South based on location.
How it is done now makes little sense other than possible some failed attempt at prioritizing rivalries over location. However, rivalries would grow stronger if they pitted teams against each other that were closer to each other. Most major rivalries in college are within the same state, not across the country.