I'd guess 3D would be very similar in execution when everything's stuck to the ground (i'm thinking in terms of an outdoor terrain engine like mine), you'd just take into account the slope of the terrain. Now if you introduce flying soldiers you would have to think in 3 dimensions!

This is a very interesting subject, I'm going to put development of my game on hold while I learn some basic AI and look into crowd movement algorithms. I remember at Uni we had a lecture in which we were told about a crowd simulation to find out how to make safer buildings. As far as I can remember, they found that in a fire, a door which allowed one person through at a time got people out quicker than one which allowed two people side by side. In the simulation, people just got stuck trying to squeeze through, but with a narrow door they went through single file and escaped.