Yes, in particular Supreme Commander fixed the lack of formation system in Total Annihilation, by implementing a new kind of formation system that would make agents keep relative formation while moving like a group. Basically, two groups could cross without interacting much because they kept rigid formation with the group.
They did some article online about that, called it "Flowfield" :
http://www.gametrailers.com/videos/tafxyc/supreme-commander-2-flowfield-pathfinding-docAlso, depending on the space structure of the game, this might not be a good approach. For example a game like Homeworld or Homeworld 2 really needs to think in attack waves. Still the ships do what they can to keep organized. It's really interesting to see because you can have different level of dodging, which means they are more or less allowed to break formation depending on the player request.