I don't even think geographically the divisions are even aligned the best they could be. And now that both Leagues rules are the same. They should be able to swap around American League and National League teams freely.
The Dodgers, Angels, Giants, A's, and Padres should all be the same division.
The Phillies and Pirates should be in the same division
The Yankees and Mets should be in the same division
Marlins and Rays should be the same division or move the Rays to Montreal and leave them together with Toronto
Both Chicago Teams should be in the same division
Both the Cardinals and Royals should be in the same division