Add in the ability to fly your ship in space from planet to planet, and the possibility of random events in space.(Meteor showers, coming across enemy ships etc.)
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I definitely think we should be able to do more with our ships, there should be missions and events that involve flying it and fighting in it, also PVP ship battles could be fun! This way there's a point in buying a better ship because it will have better armour, shields, weaponry, speed etc. I think your own ship should be very involved in PVE