That's a really fun idea... If only I had an extra million dollars lying around as I'd hire someone to work on implementing that right away.

I'd actually suggest that the 'planetary' mode (adding dust/sand/power like features) could combined with the 1st mode. Imagine a power/sand simulation in 3D with multiple bodies.

Either way this would be a lot of work but with potentially awesome results.
Here's a powder game to check out:
http://dan-ball.jp/en/javagame/dust/The atomic mode would be the most complicated since the math needed to make this representative to reality would need to be based on quantum mechanics (which doesn't really make any sense

) instead of Newton's law of gravitation (which is very simple comparatively). Either way the idea of a Universe simulator that worked on all scales from the galactic to the sub-atomic is very appealing to me.