This is a story that will involve a fair bit of flying a spacecraft. You can use the autopilot instead, but you may not be able to reach the best story endings if you over-use it.

How confident are you in your piloting abilities? This is not so much the quick-reflex trick flying, but having to match orbits, point your ship in the right direction, understand the controls and instruments and so on. 

Your choice of skill level will basically affect how long you have to reach your target and how quickly your fuel will be used up. Choosing higher levels means that you will have tighter margins and will have to fly more carefully, making fewer mistakes.

The lowest level can complete the mission, but won't be able to reach the very best story ending (because it might be too easy) and the very highest level won't have access to the autopilot at all.

Good luck and happy flying!