I think it's partly a case of that mission being too much like shooting fish in a barrel. It is intended to be more of a command-style mission - you have lots of command points, you flagship is a carrier - so not piloting it much isn't a surprise. But, coupling that with a lack of strategic difficulties in the same mission is a problem. I have to admit that this one wasn't playtested very much.
I still think it's a lovely mission, the difficulty just needs to be relabeled from 'hard' to 'tutorial'.
I think what people really what in terms of new orders is a 'flagship' command. Ie. Something that probably looks a lot like a 'defend' command that attaches itself to a ship rather than to a point in space. The problem right now is that lacking any specific orders everything defaults to 'search and destroy', which is wrong and leads to the chaotic spread of ships problem. Rather, the default behaviour (assuming you bother to assign a 'flag') should be to stay in an area around the flagship (and therefore fight as a concentrated group), with 'search and destroy' being a command you give once the mission is effectively won and you want everyone to chase down the enemy at their own speed.
In terms of 'formation', I think that rather (and this is all complete conjecture because I have no idea how you are coding the AI) than having ships try to maintain fixed positions it might be more fruitful to have ships 'want' to be in certain areas under certain conditions (which paves the way for commander 'traits' to influence where ships want to be).
For example, with no enemy ships in range, frigates following a flagship should 'want' to be somewhere out to the left and right flanks to provide protection. Fighters and other strike craft might have the freedom to move in a much larger arch in front of the formation to provide forward cover.
When an enemy force is about to be engaged (say, about 2x direct weapons range but this is completely variable) then this behaviour changes and the frigates 'want' to be moving forwards to envelop the enemy etc etc.
I don't know if this kind of thinking is helpful or not.
e: ok i saw this post in the other thread:
The reason for that is to give you the best chance of winning if you don't give any orders - sticking around by your flagship would just let the enemy control the map and then tear you apart, while going out to engage them would do better. It should also work more smoothly for a fight where you have significant superiority and just want to rush them... but that's really campaign stuff.
This is the problem we're talking about. You
shouldn't win if you don't give any orders. I don't want to feel like the game will win itself without my input, or
worse, that my input might actually make it harder to win.
I think what people want, and is in line with the new command system, is to be making the kinds of broad decisions of 'do I keep my fleet together to concentrate firepower, or do I peel off squadrons to go after that point, or do I just order 'general chase'?'
Winning needs to be about striking a balance between concentrating force and dispersing to control the map, except right now there's very little control over being able to concentrate your force so we're ending up with these chaotic melee's streching across the map.