I have tried to use the mission system. And here are my thoughts how to improve it:

1. Make a distinctiion between the GPD missions, CONS missions and pirate missions. There are no indications what missions are which. You can get the pirates mission and cons mission from the GPD station. Make some distinction on those missions as it is kind of frustrating.

2. Maybe you should add some search button to the map, to make it easier for new players to search the galaxy for the right sector.

3. Indicate how many reputation bonus the mission give.

Another issue I want to talk about is the Energy beam mkIII and its energy cost - 240. It makes no sense at all. You could as well tell that energy beam mk3 is undoable manualy as you can't have enough energy and storage in any ship that curently exist in the game.