The current system brings the chance no matter how slim of pitting both New York teams or both Bay area teams against each other in the Superbowl. It may not happen, but there is always a chance. The NBA does that strict geographical set up, so no way the Knicks and Nets will face each other in the finals or the Lakers and Clippers. None of the Texas teams or Florida teams will ever see each other for the championship either. In the NFL, it can happen. Pittsburgh vs. Philadelphia or Dallas vs. Houston. Okay, maybe not the last one.
There are only a few teams in the NFL that are geographically challenged under the current system. Probably only the Chiefs, Dolphins, Rams and Cowboys ever really have to go out of their way when it comes to traveling to divisional road games. Those teams also have some of the best division rivalries. The rest of the divisions and teams are already in close proximity.
The NFL has a good system in place. There is no need to change that.