So, to be honest.
I'm at a bit of a loss here.
Aside from the models and a few names, SAFSO isn't much like the 32x or SS game at all. And when I made that rough mission in a more 32x style (The player takes on several capital ships with little support) it was said to be boring.
So like, are we just going with a freespace style mission approach? Capital ships are 'set pieces' that are either there for story purposes or bomber runs, lots of fighters and a lot of relying on wingmen and such? Aka, the 'realistic military' style over the arcade style of the original games.