the MCU gets a sensor reading, puts it into a API packet, and sends it to the XBee that in turn forwards it to a coordinator connected to a PC then logged to file.
question: can the XBee endpoints have the sensor connected directly and forward that data to the coordinator? that is do away with the MCUs?
Yes, the MCU may be able to be removed from the end devices. The end devices do not need to be in API mode to communicate with the coordinator. The AT commands for the end device simply need to be set to communicate to the coordinator. The coordinator can then be placed in API mode if you wish, but it is not requisite that both ends of the link be in API mode. Namely, an AT mode module can communicate with an API module.