Some people are skeptical about whether this is an April Fool's prank, but it seems genuine to me, so I played the first mission.
ACT 1: The Command Briefing
Not much is here to comment on. There's only one stage that consists of a few sentences. Your language is very laconic and reminds me of Mordin Solus; while this can be a good thing, you leave out details that would help with immersion. For instance, why has a single Shivan destroyer eluded the GTVA for six months?
ACT 2: The Briefing
Again your language is extremely laconic. Concise sentences serve a purpose, especially in a mission briefing, but it just creates an impediment to reading the text. Consider the FS1 briefings; they were concise, but they flowed nicely, instead of being short, choppy sentences or fragments.
On stage 2, Beta wing's popup shows an Ursa, whereas they fly Erinyes.
Why is stage 4 its own stage? It's one sentence that goes well in 3, and no icons change.
ACT 3: Loadout
Alpha is instructed to use Maras to "confuse the Shivans", but they're not undercover and other craft can be selected. This needs reworking. There are not nearly enough Tempests- remember, a single Mara can hold 840 of them!
ACT 4: The Mission
Well, um, BEAMSPAM! If I don't disable the Ravana's beams the Aquitaine is destroyed. If I do, the Aquitaine destroys the Ravana with beams. I thought we were going to capture it?
ACT 5: The Debriefing
Well, I debeamed the Ravana, allowed the Aquitaine to destroy it, waited for a bit (There's no RTB message so the mission never normally ends), then jumped out. I got what I can only assume to be both a failure and a success debriefing- one talks about an NTF spy gaining access to the destoyer, presumably from the Omega, and one says I allowed the Aquitaine to be destroyed (protip- it's not enough to slave the "Protect Aquitaine" directive to a success condition, which I assume you did, you have to check for any end condition. This includes the "Ravana Destroyed" ending, which you don't seem to check for at all).
All in all, I think I can safely assume you never tested this mission. You seem like you have a viable campaign idea with a weird-but-doable premise, but you need some basic lessons in mission design. Do the FS2 FRED walkthrough (FS2/data/freddocs/) and look at SEXPs (in events, objectives and debriefings) from the FS2 campaign, as well as some paragons of great FREDding such as Blue Planet and Vassago's Dirge. You will learn a lot.
ONE LAST NOTE
You say you're going for a retail-length 40-mission campaign. In a word, don't. In more words, there's a lot to be learned from the campaign building process, but creating a full-length campaign AND TESTING IT- which you do not seem to have done here- takes much more patience than a lot of people have. Make a shorter campaign- maybe take these three missions, fix them up, and put them together using the Campaign Editor- and then put your efforts into larger projects.
I'm going to playtest your other two missions as well, and give you any feedback that isn't the same as the stuff covered here.