The first change I would make is the use of asymmetric key exchange. Most Zigbee implementation simply send the key in the open or encrypted using the default key. This is an easy target for attacks. If asymmetric key exchange using a random key is used, the key will also be secured. The down side is that the key exchange will take longer. Implementing this will be able to prevent many of the current Zigbee attack methods.
Another improvement could be the introduction of directional antennas, so that spatial division multiple access (SDMA) can be used. Using this technique, can more effectively reject interference from potential attackers and it can also prevent some of the routing attacks.
I.