I just did a quick playthrough, and my first impression was "wow, that's a lot of messages!" They all blew by so quickly that I was only able to read about 1/4 of them. It took me a while to figure out what I was supposed to be doing, but I'm not sure if it can be made any more clear without literally telling the player "order one of your wingmates to protect your target." When I was failing to work with query_orders, I did notice that the colonial shuttles can accept the order "capture my target," which seems close enough to what's going on that the player wouldn't think twice about it... Like I said, I'm not sure if that's any help. Also, what's the deal with the orbital stations? Maybe I wasn't paying attention, but I didn't realize I wasn't expected to scan everything I found.
I tried reading the mission in FRED, but the event titles throw me in loops! It does seem like you've addressed a lot of branching paths but I didn't really notice those options while playing it. Overall, the mission feels pretty darn solid to me. And since you requested suggestions for the "good" ending debrief, I thought it would be cool to make a reference to when Apollo shot down the Olympic Carrier in the series. The line from the series that I had in mind was "A man takes responsibility for his actions, right or wrong. He accepts the consequences and lives with them… everyday."