1) Have an "ejection-proof" check to prevent bodies from being launched by large timesteps.
If they can't be processed properly at those speeds, it would just "disable" the effect of gravity on the object and keep using the last recorded full orbit. (Moons and planets that are close enough to a large body to be ejected by a large timestep typically don't have a big gravitational effect anyway, and they surely don't influence other objects in the system if they are catapulted out at the speed of light!)
2) Calculated absolute and apparent magnitudes
It'd make it easier to judge the brightness of an object if those two were listed under the detail list that appears when right-clicking on something.
3) Have auto-orbit select the barycenter in a multiple star (or planet) system.
4) Have an option to allow barycenters and landing points to be hidden from view
Currently, I just make them black, because when I'm viewing a system from a landing point, by default it leaves a white dot in the middle of the screen.
5) Temperature-based textures.
Possibly, Universe Sandbox could have an "advanced" tab underneath the default texture area to allow the user to place temperature ranges for other textures. Universe Sandbox would then just blend from one texture to the other once the planet starts to approach the edges of two texture ranges. This effect would be especially awesome if different sections of a planet had temperature calculations. (Dynamic ice caps, even on tidally locked planets!)
6) An optional reflection map for planets
It would be really cool to make rocky bodies with noticeably varied surfaces
7) Tidal bulges based on rotational speeds or gravitational effects
8 ) Temperature changes based upon large impacts (i.e. a molten Earth if it is struck by Mars, somewhat related to 5)
9) Light falloff for dust particles.
Currently, dust is just as bright at long distances from light sources as it is when right next to them, making it hard to view dust-filled systems from large distances. Similarly, stars don't have a significant light falloff with distance, either.
10) An optional aurora effect for atmospheres
11) A label option that only indicates major bodies (i.e. stars and planets, but not moons)
12) This is stretching it, but an option to convert all bodies not contained within the nearest solar system into a background texture.
Basically, if you selected "Convert to background" while viewing our solar system, any other solar entities are placed onto a texture sheet that can be used as a stellar background in Universe Sandbox. That way, someone could create their own constellations and galaxy placements without being overly taxing on the system.
13) The ability to place reference points on a background image, effectively allowing stars to be labelled without needing them to be processed in the physics engine. Of course, that means that you couldn't zoom in on them and view space from their point-of-view, but it could help out low-end systems. (ties into 12)
14) An infrared viewing mode.
15) Orbital and rotational options to make it easier to achieve resonances. (Other than 1:1 tidal locking, of course)
16) Satellite and spacecraft models.
It's been mentioned countless times, but it would be very cool to view space from an object with a controllable velocity!