Mostly a huge suggestion dump:
Plane Tilts
Essentially an option to change the inclination of all/selected orbiting bodies proportionate to their distance from parent, instead of having to manually change every orbit to match the tilt of a body. Not sure how easy (or possible) this would be to develop.
Wormholes
I think wormholes are a must-have for any space sandbox. Basically, wormholes could be selected and re-rooted to other wormholes.
Dustballs
A place-able spherical or circular mass/disk of non-attracting particles to experiment with the gravitational gradient.
Random Galaxy Generator
A menu of objects based on the Hubble Classification System. Selecting from E-, S-, SB-, or Irregular-Class galaxies opens a menu of parameter to set, such as Max/Min distance from core, Number of arms, Total Mass, Single/Binary core, etc.