I don't know if anyone has said this, but the ability to build the payload and rocket separately. I typically use variations of 2 - 3 rockets of different size / range to launch everything, just switching out the payload. (I do occasionally switch out the upper / kick stages for longer range. I tend to build smaller things, so NERVE is great for sending 10 tonnes to Duna.)
I know a lot of us want life outside Kerbin. People seem to like friendly sentient aliens, but I really want a pet of some sort. (a dog that follows you around and sniffs out stuff would be an interesting mechanic.) Life of any sort on about 1 planet from every 10 systems would be great, if it was varied enough. A black hole system might be interesting too. Not sure how you'd simulate that, but please give it a shot, Intercept! You can add content to the game with updates! We don't mind!