Looked it over in FRED, and spotted a few things. In no particular order:
1) Admittedly a very minor nitpick and not one that affects the mission. There's no need that I can see for 4 seperate events to cap waypoint speeds, you can just use 'add operator' to fit all 4 of them into the same event. Makes it easier to get an overview of the events if you later revisit the mission if there are less of them. But really, I guess this one just comes down to personal preference.
2) AI-chase has a tendancy to cause a nasty mess when used for capships. It's preferable to script any capship encounters instead of letting the AI sort it out.
3) I'd also advise against using are-waypoints-done-delay for capital ship, as they sometimes miss them due to poor turning rate and end up circling the same point in space forever. Using a distance check against the last waypoint is safer.
4) Nice to see properly done directives
5) Everything is on a 2d plane. Don't forget that space also goes up and down. Only possible exceptions are the random arrival locations of two wings (which, btw, I was very happy to see... people too often keep them all fixed making things just a bit too predictable on later tries). Even just shifting a few of the civvies a bit up or down would be nice for effect, and would be enough to make it not very noticable.
6) Another minor nitpick. There's no need to turret-free ships unless you locked them previously - They're free by default. It's just beams that need it.
Sorry... I just can't help myself when I see FRED topics
**slinks off, hoping Karajorma doesn't mind the intrusion too much**