OK, I haven't finished it yet, but already I have a few complaints/suggestions...
You have a lot of well done mission chatter. This is good, very good. However, some messages go by just a tad too fast. I'm sure you don't have any problems with it, but people like me who don't read nearly as quick would rather not have to constantly have to press F4 to catch the messages that just went by. A way to help solve this would be to have the game play a sound whenever a message appears. (emptymsg.wav works quite well.) This would also help to attract the attention of the player to the messages during battle.
In Hmsk-B6.fs2 ("The Draft"), the GTC Shield's engine can be seen blazing away with all its glory. I find it difficult to believe that the engine has been on for over thirty years. Maybe you should have the Shield start out disabled, and then have the engine 'reactivated' by the recovery team. Just a thought.
In Hmsk-C1.fs2 ("Return to Oz"), your red alert event executes prematurely. I say this because the following happened to me: The Custodian had just sent the message that it and the Shield were ready to depart. However, I was already at the node and the red alert event triggered before the corvette and the cruiser departed. Because of this, I was forced to repeat the mission. I believe what you want is to have the red alert event trigger only after Alpha 1 has reached the node and the two ships have departed, not just when Alpha 1 reaches the node.
In Hmsk-C4.fs2 ("Ram Raid") the appearence of the 'Depart' directive is premature and misleading. What happened to me is that I had just finished off the Dispatcher (the Tefnut having completed its task) and the Mammon arrived. Then the message to retreat was sent by the Custodian (I think.) The 'Depart' directive appeared and I hit my subspace drive. Not only did no mission debriefing appear, but I was not allowed to moe on to the next mission. I'm not sure what's wrong here (I haven't beat the mission yet, I need to do it again) but you should really change when 'Depart' appears. As I mentioned before, it's quite misleading.
So far, I've enjoyed your campaign. Personally, I think the flow of some of the first few missions might have been better achieved by using a long chain of red-alert linked missions instead of making pit stops in systems along the way. But aside from that: hats off to you! I've yet to download your Inferno campaign, but I'm looking forward to that as well. I hope I've been of some service.