Your idea kinda sparked one in my head. While the wand is cool and would allow direct interaction with your solar system, it is similar to the dispenser under the "powers" tab. I do like the idea of terraforming mountains or craters, though.
But this is what I had in mind. Since Universe Sandbox 2 has some simple height maps already in place for planets and moons, they could add more sliders under the "materials" tab on the property window. Right now, we have sliders for hydrogen, water, iron, organics, silicate, etc.
What if they added sliders for mountains, rivers, oceans, lakes, and craters? For mountains, you could adjust the severity or texture of the surface. Or maybe a slider that allows you to change how big the mountain range is. Do you want it to be a sprawling, unbroken mountain range, or a varied range with valleys and breaks in the terrain?
Rivers could be similar. Maybe one slider could adjust how much tributaries taper off, or one could change the width of the river. I won't go into detail about the others, this should give you the gist of what I was thinking.
Plus, I don't think they would need to change much to get something similar to this to work (I could be wrong though). Giant Army could keep the way they have the height maps and figure out a way to simulate generating different textures on the surface. I wonder if they would be able to procedurally generate textures for planets outside of random planet spawns? Like so you could terraform the surface in more detail even after the planet has been spawned.
Just a suggestion...