Just finished this a little while ago. Very good overall. Good mission design, and some interesting dialogue and story.
That said, it's a little rough around the edges. There are several little things that I think could be improved.
In Amenophis's meditations, it's not really necessary to have (cont.) at the beginning and end. I don't need to be informed that the next briefing stage is being spoken by the same person. I only need to be informed when the speaker is changing, like if you started with Amenophis meditating and then switched to someone else giving information. And in that case, you'd just put some kind of title at the top of the briefing stage when the speaker changes. In my opinion, the (cont.)s are awkward and unnecessary, and this really stood out in one or two command briefings where I scrolled down to find that the only thing there was (cont.).
The same goes for mission briefings. You don't need to put "Runihara:" at the beginning of every paragraph Runihara speaks if he's the only one speaking in that briefing stage. I assume it's still him talking until something tells me otherwise. At most, I'd put Runihara's name only at the start of the briefing stages where it's just him speaking.
In-flight messages are going by way too fast. It would also be good if they had sounds. I don't mind reading text, but I do like it when I'm given some kind of audio alert to let me know there's a message, even if it's just one of the generic message beeps. Adding some head anis to the messages would also help. Black Wolf's Vasudan anis could be put to good use here, especially the ones where the Vasudan is wearing sashes.
Briefing icons would be good.
Now for a few mission-specific things:
There was a very long delay on the Revelation first going hostile after the Apocalypse destroys the Emissary. At least ten seconds between the Father telling me to execute them as traitors and their IFF changing.
In Pergamum, Cheops and Madu somehow died long before their dialogue had finished. I never actually fought either of them at all.
For the second-to-last mission, you might want to make it more clear that using the Sekhmet isn't strictly necessary. The first time I played that mission, I assumed that I'd have to take down capships at some point, because I was being given a bomber and torpedoes were available, so I loaded two banks with Cyclopses only to find that it's strictly an anti-bomber mission. I ended up using the Sekhmet anyway for its missile capacity, but took Tempests instead to take down bombers more quickly.
The briefing for the last mission tells you to do the wrong thing. You're told to only use torpedoes on corvette class ships and above, but that is plainly not what you're supposed to do. I'm not saying you should tell the player exactly how to win, but telling them to do the exact *wrong* thing isn't a good idea either. However, I did appreciate how the briefing informed me which wings were bombers.
Also for the last mission: Giving us command over every single wing probably isn't necessary. I had my hands full just managing all the bomber wings. Having all those other wings under our command just clutters up the comms menu. On the other hand, this could also be a deliberate design choice on your part to increase the challenge level of the mission and force the player to use more advanced gameplay elements like ordering wings with hotkeys. You pretty much have to use hotkeys to command the bombers effectively. That's a legitimate design choice, so if that's what you're going for, I'm all right with it.