If I may, I'd like to see an Faster Than Light style free-exploration/trading game where you have a rotational 3d ship that can be viewed in layers, where instead of clicking on the single crew member you click on the system that needs repair and prioritize repairs by balancing the manpower. Any 5-year mission is going to see a formidable ship presence into the multi-verse, so as long as you have people to conduct repairs and the necessary materials, you're going to be able to make it back to Stardock. Answering distress calls, sending your shuttle down to planets when transporter is in operable, and beaming chief officers and security squads into planetary installations and abroad enemy ships mid-combat, fighting the odd gravitational pull when powerless.
Something similar to Elite
albeit with a little more complexity?