I'd like to see a bit more realism:
ullage, limited relights depending on tech, maximum burn times, lagrange points, saturating reaction wheels, more realistic reentry heating, improved science and better aerodynamics
And some easier bits:
An ingame way of building encounters so we can figure out slingshot courses etc without external tools, programmable autopilot for autonomous landings and booster recoveries, built in alarm clock and an ingame delta-v map