/3/ - 3DCG

Right now it seems like you have a lot of polygons that aren't visible because they are intersecting, so that's a huge waste right there.

You could try a polygon reduction algorithm, I think all major 3d packages have them. Not sure how well that will work. The individual spheres don't look like they have a lot of detail, so you might be left with a jagged mess if you reduce the geometry too much. Might be enough though?

Personally I'd do this with Houdini. You can convert the whole mass of spheres into a volume representation and then convert it back to geometry with complete control over how many polys you end up with.