Based on my experience of nearly one year involving in the development of hexacopter platform powered by Arducopter firmware, I have discovered that if the hexacopter is able to perform well in altitude hold mode followed by a good loiter performance, it wouldn't have much problems to be flown autonomously. If you have problem on that, probably one of the tricks to solve it would be try setting up the "Throttle Mid Position".
Initially, I was using six 2212-13 1000kV brushless motors with 10x4.5 props which gave me a decent thrust of 0.6kg each. During its first flight itself, the platform was able to hover nicely at 50% throttle. I only had to tune the altitude hold P value for better performance. After several crashes during following flight tests, eventually the motor shafts were severely bent.
Then, I switched to Tiger Motor MT 2216-11 900kv brushless motors. That time, my air frame weight was a bit higher (nearly 2.6kg) with additional payload attachments to the air frame such as video transmitter, payload drop mechanism, landing gear, camera and some optional components. During its first flight it hovered at 70% throttle. When I switched to altitude hold mode instantly, it would just shoot up and when I position throttle at middle, it descends.