Im agreeing with OP completly, please dont change it away from how it curently is.
If there is any plans on implementing some form of Space PvP or more Open Free Movement Space missions, add them on the side of the curent system, like being able to either go the curent On Rails missions or Railless missions.
Just, please dont remove the way they work right now, really love it alot
That being said, it would be cool with some minor things added. Like a Mission Completed summary showing how many Enemy ships destoried, how many turrets, generators, engines etc etc on enemy capital/destoryer's/space stations blown up. Maybe even make it so the system shows how many out of the amount total on the mission.
Ex: X amount of enemy ships destoryed out of 100
or on the mine field missions how many Mines out of the total on the map destroied ^^
would be fun to compete with yourself or friends over how much you manage to blow up per mission
but yeah, going to say again, being a person that dose all the missions several times a day over more characters, please dont change the current system from how it works, really enjoy it alot!