While the parts are in the mail, we started working on our remote controller. Most hobby RC quadcopters are controlled using a standard RC radio. RC radios typically output PWM signals, which can be connected directly to servos and motor ESCs. Because of this, the MultiWii board and software we are using is designed to take several PWM inputs as RC signals.
We don't have an RC radio, but we do have two Xbee radios, two Wii Nunchuks (with adapters), and a spare Seeeduino Mega. Luckily, the MultiWii software can also accept RC signals over UART as well as PWM, so it should be possible to build our own (primitive) RC radio controller.
Connecting more than one Nunchuk to an Arduino however, is nontrivial. Nunchuks connect to the Wii remote over an I2C bus, but all Nunchuks have the same I2C address, meaning that more than one of them cannot exist on the same bus at the same time without causing problems. One solution is to use transistors to connect and disconnect the Nunchuks from the I2C bus dynamically so they don't conflict with one another.
This solution worked perfectly. We wired it according to the diagram in the linked post above, using 10KΩ resistors.