Give Astronauts the ability to gain experience. An experienced pilot of all vehicle types can give bonuses like: -1% fuel burned, -0.5% less heat and collision damage, +2% engine ramp up speed, +1% extra engine power, -0.5% effective mass, etc
The experience can maybe be gathered from missions/contracts, or from an astronaut's personal milestones, etc. I think this would give certain astronauts more value, and would make rescue missions, having pilots returning safely, a lot more compelling.
Another thing I'd also like to see is astronauts retiring. So we get a good rotation of astronauts instead of the same 10 ones going here and there.