I belive alot of it had to do with the actors. Alot of long hours and such were really taking there toll, they had been doing it for 7 years. I've personally felt the actors weren't as willing to put up with things as much since Amy Sherman-Palladino had left.
The reason is that Amy-Sherman Palladino and her husband could not come to an agreement with the WB network for whatever reason. So Amy and her husband left the montrer and the WB network only continued it on for one plus season.