The spaceplane autopilot has very little variables the user can control. That sometimes makes it difficult to use it. Some critical situations I've identified:

• getting a large plane with not too much reserve thrust to altitude, it will stall because the autopilot pitches it up too much
• flying a plane at high altitudes where small steering inputs can fling the plane out of control or above engine flameout altitude
• getting an airplane with little roll or yaw stability to fly a certain course

Some features of real autopilots would help, some of them are already in Mechjeb and would only have to be extended to the spaceplane guidance UI:

• set/limit angle of attack
• set/limit rate of climb/descent
• set/limit IAS
• roll turns instead of yaw turns (the new aerodynamics make yaw turns as unpleasant as they are in the real world
• control over steering factors to dampen down control input on jumpy planes

You can probably get some ideas and input from either FlightGear (which is C++ admittedly, but programming, like love, is an universal language) and/or BD Armory which has marvelous plane and missile autopilots.

I am afraid this is not high on my list for now.
The last dev has a few change that may help with jumpy planes however (with AutoTf enabled)

Please note the screenshots below. I assure you that the spaceplane had plenty of control surfaces and reaction thrusters to control its attitude at both half and twice the altitude. I have to consider the attitude mechjeb steers that spaceplane to a bug. Mechjeb acts as if the spaceplane is a rocket that can just be stood on its tail, thus flaring it terribly it and wasting all forward speed for an error of a few hundred meters altitude. (Originally it was supposed to bring the plane from 38000 to 40000m) That's why I'd consider a "limit AoA" option an absolute minimum to make the spaceplane guidance work reliably.