I have a bit of a wish list for features. I would like to see:
Auto-staging: This would allow for time delays inside of stages, or conditionally make the craft remove the next stage at the current stage's completion. Adding auto-staging would create better autonomy in getting into orbit +/- other planets.
More RTG options. The small PB-NUK is great in a pinch, but there should be more of them.
A "Remove Object" button that will allow you to jettison parts in space. One reason this would be helpful is to cut down on weight as needed. Also, I removed a mod and I used a part from that mod on one of my ships, so after restarting my game, I was dismayed to see that all of my ships were gone because of "missing or unknown parts".
I will add to this a bit, so please follow this discussion