I have found that even without fancy code, the thermopile is a surprisingly robust solution; a LOT of bang for the buck. This keeps my AttoPilot in the spirit of "simplest low cost 3 axis autopilot.
My first flights were with very stable aircraft (the Miss2 old-timer). Even with this plane, over-steering was a problem at times. I realized some method of attitude sensing was a strict requirement for any serious autopilot.
I started out flying the FMA CoPilot [which is based on the IR sensor show above] only as the typical RC usage on a small unstable homemade plane with no dihedral and just aileron/elevator flight control. After experimentation, I realized that AttoPilot could skew the inputs to the CoPilot control box, and all of a sudden I had AttoPilot flying that same small unstable plane (at 70+km/h) even better than the raw AttoPilot used to fly the polyhedral winged Miss2.
Later, I reverse-engineered the CoPilot sensor head, and figured out how to interface to it directly to AttoPilot via 2 channel ADC (BTW, there is mis-information on the Paparazzi website regarding the FMA sensor head; it say CoPilot head is designed for 5V, but in fact it is actually a 3.3V device, so you don't need to replace resistors to make the gains correct), so now AttoPilot has direct use of the thermopile data, and therefore has direct idea of pitch and roll angle for a robust flight control solution that will never over or under-control.
I am integrating GPS and barometer data with the thermopile, so the solution is very robust, and self tuning. Additionally, although I have a working Kalman IMU, accelerometers have the limitation of being affected by motor vibration, whereas the thermopiles are immune to vibration.
So, in the end, to keep in spirit of a low-cost full function autopilot, I am starting out offering the thermopile version. As I wrote above, my use of thermopiles is more sophisticated than FMA's, so people should not be fearful about how well it will control their plane. I do have a working Kalman IMU, but just not ready to a level that fits my vision of a plug-and-play autopilot. Building all of the fancy control routines for my usage of CoPilot thermopiles is a nice stepping stone to a Kalman IMU later.