This is sort of hard for me to post. I don't mean any ill will toward you or trying to tell you how to make a campaign, but this campaign is not at all what I was expecting.
I have played it from start to finish. Both branches, though I took the Character Branch first through the campaign, then did the Military Branch through the tech room.
I want to start off by saying this was quite the undertaking. A lot of effort went into this campaign, building a universe mostly from scratch. Everything was reworked. New weapons, new tech room entries, all the fluff that you'd expect with a large campaign like this.
I am afraid this is where its going to get nasty. I have total respect for you and what you've created, but here is my honest opinion.
The missions were a mixed bunch. A lot of them were simplistic, and there's nothing wrong with that. I enjoy blowing stuff up.

But others were minutes and minutes of talking and talking and the player doing one action to justify him being there. There are missions that go up to 8 or 9 minutes in length where the player does nothing. All he does listen to people talk. I could go mission by mission, describing all the things that annoyed me, but at the risk of sounding mean and uncultured, that would fill up quite a bit.I'll just go through stuff that really stood out. Spoilers abound!
I think my fears started to come up in the opening cutscene. I am treated to a picture of a planet as subtitles describe the situation. I was a little annoyed at how that's all the camera movement there was, but the thing that hit me was the line "It's propaganda." That started DoS's way of telling me how to feel.
All throughout the campaign I get messages in second person telling me that "You like the sound of these guys" or "The Admiral's words do not affect you." To quote Futurama (of all things), "You just cant have your characters announce how they feel! That makes me feel ANGRY!" Why am I being told this? Why can't I come to the conclusion that these guys are giant assholes or if they're sent by God. "Show, don't tell", is a big rule in writing.
Speaking of writing... When I was testing WoD for Spoon, I complained to him that his chatter wasn't strict or military at all. But as I played through, the entire mood of the universe felt right for that level of "light" chatter. But here the writing... it's as if everyone is a complete and total jerk. The dialogue is so unprofessional and at times, painful to read. I didn't feel as if I was in the military at all, more like a part of a mob led by the scum of humanity. If that's the sort of thing you were going for, bravo. I couldn't identify with anyone, not even the player character (especially during the character branch).
I don't see how humanity got as far as it did with this level of hostility amongst itself. You've got pilots saying things that would get them thrown out of the military, you've got Admirals who casually dismiss the value and importance of anyone under their command. How has the military not devolved into a total state of anarchy? Judging from the "protestors" it looks like its almost at that stage.
Anyway, here comes my critique of the story as a whole.
It started off alright. Rebels from the virus-ridden planet are waging war against the iron fisted military. Soon we meet the Vasudans and first contact doesn't go too bad (we're not killing each other YET). But then we start fighting and it starts going down hill.
I think what sealed my opinion on the campaign came at The Return. So we're finally able to target Vasudan fighters. We kill a wing of 8 fighters. I was sort of pumped! The story wasn't doing it for me, so I was hoping for some mindless action would get me going. Then a Vasudan corvette jumps in 10km away and Command says "I want this to be a fair fight." and sends in his own corvette. So I get 5 minutes of watching two corvettes blob spam each other. If that wasn't annoying enough, I got a training message saying "Use of time compression can screw up the mission balance."
I thought it was cute the first time I saw a message telling me to use time compression because the rest of the mission will take awhile. But really now, you're making me do nothing for 5 minutes! There's barely any chatter, there's no beams, no missiles, nothing exciting happening and you're suggesting that I spend my time doing nothing. WHY?
When I hit Dealing in Extremes, I was sure this was going to be the payoff. From the briefing, this looked like the archetypical moral dilemma. I am ordered to murder refugees infected with the virus. This is where I am allowed to exercise my own choice and decide if I really want to be part of this tyrannical force, right? No, the very first line of the mission comes from the player character saying that we should split up to finish them off faster. The PC then goes on to say remember to use your secondaries. Since it's clear I have no choice in the matter, I partake in the slaughter of innocents. The last transport attempts to surrender, but command says "Orders are Orders." So we're ordered to stick around in case more refugees dare arrive, and half my wingmen start protesting these orders (Nice job protesting AFTER you've become an accessory to murder, but to their merit at least THEY come around to it at all). They are then declared traitors, and I have to kill them! And then when I return to base I get a medal, Unpitying Killer! Are you serious? Could I be told that this military is worse than Hitler any more heavy handedly?
Well from the training message telling me that I couldn't believe what just happened, I... couldn't believe what just happened. The private log made it clear that maybe I shouldn't have done that. My hopes were starting to get up a little higher. And in the next mission, I saw it was time to choose the branch. Character or military. I went for character first. I thought "ok, this is where my character realizes that serving an evil and corrupt organization is wrong, and I will atone myself by aiding the people I murdered."
But no, the character branch is about going deep into Vasudan territory along side a very elite squadron, and orchestrating the death of one of the elite squadron's members so that I can take his place. You weren't kidding when you said THAT was the darker path. And then when I did "kill" him, and I joined this squad, the campaign ends. Zero resolution to the war. Zero resolution to the virus. Zero resolution to everything. Well at least I got a campaign completion medal anyway.
Ok, maybe the Military Branch will give me some more closure. I'll warn you I didn't play this in sequence. It was hard to keep track of which missions I played before without any mission numbers in the file names. But I did get through it! So the first mission throws me into a completely new character, Overlord Lahma. At first I thought he was a Vasudan, since so far we had just seen two races. Now there was that mystery ship in the subspace tunnel, but since this ship didn't look like it at all. I thought it was some elite Vasudan fighter. So after single handedly killing 3 wings, a cruiser and a science ship, it becomes apparent that I am some very powerful third race bent on ensuring that the Terrans and Vasudans die horrible deaths (I started calling this race Shivan-Overlords at this point).
Then we get a mission chasing after refugees into a nebula only to find everything is derelict and I keep feeling weak and then normal. Then we get some passing mention an antidote has been found for this virus (those refugees could've waited! but, NO, they were too early!). Then we get battle of the moon part 1 and part 2. Then we get a "kill the protestors" mission again, only for the Vasudans to show up and then the military and the protestors join forces to conquer the alien threat. Then right after, we go back to killing each other. Sigh... There's also this prophet guy who gets a quote attributed to him later.
Then we head into the home stretch of the campaign! We make peace with the Vasudans by attacking suspected Anti-Human Vasudans and show gestures of good will! Then the Vasudans take us to a cargo depot, where Shivan-Overlords (where I am told they are called the Manipulators) suddenly come out of nowhere and kill everyone. Then I watch as my command ship is destroyed by the Manipulators! Then I watch as the last remnants of Terrans and Vasudans make it to some large complex with other alien ships (including Shivan Ships). And then we pan to a Knossos and... end campaign I assume. I didn't play this in the campaign room, so maybe I'm missing something. But that IS the last mission and there is no debrief.
I guess it's a cliffhanger...?
Sorry if that comes off as rant-ish, but I couldn't take the campaign seriously after Dealing in Extremes... Everything felt just so empty. My actions did nothing at all. That's fine for a cog in the machine sort of thing, but it left me without any sense of accomplishment, which I think it important to the player to feel.
I think the worst part of it was, this was not the campaign I was expecting. Maybe that's why I am not a fan of it. When I first heard of it, I thought it would be like Deus Ex in SPAAAACE. Iron fisted government with a virus-ridden population on the verge of rioting. All I got was
FS1 remade with Nightmares instead of Shivans.
I thought the branches would be based on the morality of the player. Either the player must choose to enforce the law that he swore to uphold or join the people being oppressed. All I got was being a cold blooded killer with zero choice in the matter.
If you're looking for suggestions on how to improve this... I don't know how you could improve it. I don't know how you wrote the story, but I think you need to find someone who can go "This stinks" to your face and pitch them ideas. Then when they say "that's awful" you rework it until they go "that's better!" Don't underestimate that power. BP2 had high expectations, but the WiH alpha that Darius made... well. It was reported to be pretty bad. The story was very different from what it is today. The BP team saw how bad it was and told Darius how bad it was. He took it well and they refined the whole thing into the great experience that it is today.
So don't give up on making campaigns! Find a way to get feedback quickly and effectively. Get some outspoken, active beta testers who haven't participated in the developement and can have a fresh view on the missions and storyline. You've got the technical talent, you just need to practice the literary talent!