Personally I think that the idea of keeping the microcontroller and sensors on separate boards is preferable. Sensors technology evolves much more rapidly than uC. Having a solid uC base board means that the code base can be stable and people can experiment with all kind of sensor boards as extensions.
For the uC side, the ArduPilot Mega seems do have already done everything correctly (except for the price
What could be done is create a board similar to a Teensy++ but with connectors for a MultiWii application. Then a 2nd sensors board that could plug into the base one in a piggy back fashion.
Just food for thought, there are many many options... Good luck with your project