I think controls/navigation is the biggest obstacle for an average player right now and can easily make them abandon the game. You should make "fixing" them number one priority. I could easily see myself sinking 100 hours into this if controls were "intuitive".
Let me suggest the following. It could seem strange at first but may actually work in practice.
Have the camera orbit fully relative as I already suggested. Discard roll and map yaw to A-D and pitch to W-S. Now the fun part. Don't steer in ship space but instead steer in camera space. Since primary goal of steering is to turn the nose towards wanted direction, this control scheme will do exactly that from player's viewpoint. The steering becomes completely intuitive without any need to mentally keep track of how the ship is positioned towards camera or towards any absolute planes.
There are two sub options for the camera when steering this way. The camera can stay put or it can follow the steering rotation with its orbiting. Perceptually, the former will make the environment static while the ship will rotate, while the latter will do the opposite. It needs to be tested which works better, or it can be an in-game option.
This will make both camera and steering, relative to the view and completely intuitive as your control directions map to directions you see on the screen.
You can now eliminate the horizon and the axis markers around the ship. The only thing I'd draw is a simple line going along ship's forward direction from nose to the end of range. This may help visualizing where the ship is aimed.
A cosmetic roll can be kept for both; map Q-E to ship roll and middle button + sideways drag to camera roll. The ship roll happens in ship space and camera is not reacting to it.
As for auto-pilot, it doesn't need to be lock-on. If you click on the target its current position in space is memorized as auto-pilot's aim. The location is not locked/updated to the actual enemy. You'll need to click again. This works similarly to your current pip mode just that you can click on the enemy. I don't know how you currently calculate the pip position but I'd do it like this: if an enemy is clicked, use its position, if empty space is clicked, use the farthest intersection point between mouse ray and ship's range sphere.
I'd still consider full lock-on autopilot option for people who need babysitting or have poor spatial perception.