Rather than have him be an alien or something, I'd rather he just be a giant, mutated ant with super-powers and human intelligence.  Like everything else, we don't have to go into some long, tortured explanation for why this little guy exists in our world, we just put him there and use him.

Earlier, I had discussed forming a superteam of Mightor, Space Ghost, Birdman, and a few others.  Atom Ant should definitely be on that team.