There are already many good basic multicopter controller boards on the market. Think of Naze32, KK2, etc. Then there's also great firmware, some of which that support multiple boards and PID controllers (e.g. Cleanflight). Most of these boards and firmware fly great, but lack or have poor navigation support (alt/GPS hold, RTH, etc).
On the other hand we have Arducopter which is a multicopter controller that also has very feature rich and stable autopilot capabilities.
Wouldn't it be great if users could pick the basic flight controller of their choice and combine it with the autopilot of their choice? I'd like to do that, and I'm convinced that once these modular designs start appearing, that it'll boost both the development of both basic controllers and as well as autopilots.
What I'm thinking of is an autopilot board that acts as a PPM-sum filter between the RC receiver and the basic flight controller (e.g. barebones Naze32 or KK2), and has it's own gyro+accelerometer and I/O connectors for PPM-in, PPM-out, GPS+nav, and that's it. The autopilot need not even know how many motors the flight controller controls. It only has to be told via some configuration tool, what the functions of the various channels are and have configurable navigation PIDs.
If the autopilot/navigation board is designed small enough, then it can be simply stacked above the flight controller board and added at a later stage after the frame has been tuned.