You could consider looking for research autopilots. Researchers try new things in all levels of the autopilot, and so they need extensibility and performance more than advanced features.
From what I understand Ardupilot and PX4 are popular. My university uses ROSflight, which is nice because it interfaces with Robot Operating System, which allows for sensor and control data to get around relatively easily. Depending on the type of UAV you're using, you would run ROSplane or ROScopter on top of it to provide higher level functions. It is all highly extensible, and you can replace any of the layers of the autopilot independently. Also nice, it has a pretty good simulator so that you can try fancy stuff without crashing a real UAV. Do note that it lacks some of the higher-level features provided by other autopilots, and so you'll have to look at what you want to do to decide.