I'm unlikely to be able to find time to do any programming any time soon, due to a new job and an upcoming wedding, but I have been contemplating a large system challenge.
Namely, how to generate a broad spectrum sandbox arena, that is manipulable at various scales.
The example of this that I contemplate is the generation and simulation of a solar system that works on the interplanetary level, but is also manipulable on the human level, and potentially smaller levels.
Solving this challenge would in my mind include beginning with the formation of a solar system from gasses, and extending to the point where a user could dig a hole in the surface of a planet and have a material that reflects the composition of the material that would be present at that place in the system, and for the absence of the removed material to create a hole on the planet. I would want to be able to have solids, liquids and gasses that because of their inherent properties create land, seas, and atmospheres. This could be extended to include rudimentary tectonic and erosion cycles.
It seems to me the first step is implementing a system of elements, perhaps an abridged periodic table, or a fictional set.
With that in place I see this being solved by using floating points of "Pseudo-Atoms" that work like fat globules. A homogeneous mass of a single element would be grouped into one floating point that tracks the mass, which defines it's diameter, as well as vector and spin. This would allow you to have, for instance an Iron core to your planet that can be tracked as a single point, rather than having to calculate all of the component pieces of iron.
This would of course give an appearance of a bubbly foam to the surface of any object if you drew a surface at each atom's diameter, but a skin could be applied to surfaces to resolve that, and ease up the computational work needed to draw spheres. Some form of stabilization could be used to know when a collection of atoms do not need to be checked.
What I like about a system based on this is that it lays the groundwork for having some form of working chemistry within the same system that provides day night cycles, and world ending meteor strikes, all functioning off the same system.
This could become a very processor intensive simulation, dependent on the resolution used, but I'd be interested in discussing the potential that a system like this has, and what some of the biggest challenges would be.