A complete rewrite on Freespace would be awesome. At least change the look a bit more...
Anyways with AI, you should have a set distance between the midpoint. This should help you when you want a formation flow. Generally, you have an optimum distance between two ships of the same class. Divide that distance in half. When two ships are mismatched, the major ships will not collide; so for example a Deimos will never collide with a Colossus because the Colossus is set to have what would be half of the optimum distance next to another Colossus, plus half the optimum distance next to a Deimos. It keeps them separated while close without requiring so many individual settings. Add in a key for FRED to change the midpoint distance of individual ships.
Some other problems... how fast will ships move away from each other? Have it based on ship size once again. If equal class, they move apart from each other at a ten-degree angle (5 degrees off endpoint for each). If mismatched in size, the smaller ship moves away at a twelve-degree angle. Add in conflicting directions, modifying the into-formation setup so the large ship will go up and then down to meet formation.
Other things about fighters... add in a few meters differance as it always annoys me how annoying their tight formations are. Also, allow two different form-on-my-wing commands; one for stay on my wing no matter what and one for defensive formation.
That will however expand the commands system; seperate orders into three categories... Offensive (destroy target, disable, disarm) , Defensive (tight formation, defensive formation, protect target, ignore target), and Strategic (depart, rearm, capture, etc)