I've found myself stuck on the third mission for the time being, but I do have a few first impressions I thought were worth listing.
--First off, unlike a few other people have mentioned, I didn't really have any trouble at determining who I was fighting or what I was fighting for. However, I think this was primarily because I went ahead and read some of the background information on the hosted site; if I hadn't, I probably would have been somewhat lost. Since you are essentially introducing a new universe, I think some sort of in-game overview of the current situation would go a long way, whether it's via intelligence entries in the tech room, an extended initial command briefing, some sort of opening cutscene mission, use of the fiction viewer, or whatever. On a slightly-related topic, the lack of debriefings felt kind of jarring; I think they'd help add a real sense of what you're accomplishing.
--I had no real problem with the in-mission dialogue; it got a few chuckles out of me so far, and the characters seem to have some room to be fleshed out as the story progresses. However, I think using the message start and end .wavs would help a lot, since certain sequences had several lines of dialogue flying by at once, which got a bit difficult to follow. I do think that it's the sort of script that would really benefit from voiceacting, if you guys decide to go down that route.
--From an aesthetics standpoint, I
really like the ship designs you guys came up with, especially those Earth Alliance cruisers and installations. Giant ducted fans? Awesome. (Except when they manage to splat me.

) The fighters look very feasible for aerospace craft, though I'd have to assume that they have some sort of anti-gravity action going on, since they don't look like they could support themselves aerodynamically. I didn't mind the thunderstorm effect much at all; it may not be a whole lot like the real thing, but it's certainly closer than FS2's nebulae were to the genuine article. I like the weapon effects, though the capital ships' turret sound is a bit grating. Like someone mentioned before, the background image for the briefing screens was kind of distracting. I do think that coming up with some sort of custom HUD and soundtrack could have helped make the experience feel more immersive, but you guys may not have anyone on the team to handle that sort of thing, so I didn't see it as a huge deal.
--For the missions in general, I think cutting down on the waypoint-following time at the beginning would help matters, because that gets a bit trying to sit through again after dying. Also, I don't think the player is ever specifically ordered to follow Alpha 1 at the start, although that becomes sort of self-evident when you notice what everyone else is doing. I already mentioned the lack of briefings, but even the means by which the missions conclude seems a bit inconsistent: it isn't really made clear that you can't jump out yourself, and I think only one out of the first two mentioned an autopilot engaging. Making that a bit clearer might help matters.
Now, for the missions themselves:
--Mission 1 was, to put it mildly, kind of brutal. I flat-out died my first time through by getting thwacked by said installation fan, but I probably would have anyway from the massive fighter presence; as it was, I only made it through the second time around with all of 7% hull remaining. I don't really mind the hulls being so weak to missile fire, since that feels like it fits in with the pre-FS1 era you're working with, but seeing as how that's the case, I think you guys went overkill on the number of enemy ships in that mission. Cutting out one or even two whole wings of fighters would have gone a long way toward making things less frenetic, and definitely would have felt more plausible. Another element that didn't help matters was that all of your wingmates seemed to remain set to "Guard Alpha Wing/1," without you having the ability to change those orders; the AI seems to fly much better with plain old "Engage enemy," which I think would have helped take some of the heat off the player's back.
--Mission 2 was a welcome reprieve after I just survived mission 1 by the skin of my teeth, but I almost feel like it swung a bit too far in the other direction. You have large fighter superiority in the mission, and after the enemy fighters dispatch, the cruisers become nothing but cannon fodder. Even before the bombers showed up, my wingmates had managed to take out one of the enemy cruisers; after that, it was a flat-out slaughter. I'm not sure exactly how to change that for the better based on your mechanics, but there has to be something you can tweak to make the mission not feel like it plays itself.
--As for mission 3...well, I haven't managed to beat it yet, and I'm starting to suspect that something isn't working as it's supposed to there. The earliest part plays all right, when you're taking out a few enemy fighter wings, but when your friendly cruisers reach the end of their waypoints, they just stop there, with no explanation given. Then, all of a sudden, one comes under attack from an enemy ship that you can't even see yet, and even when it's destroyed, absolutely no one in the mission remarks on it; you'd think that Command or one of your wingmates would be shouting out alarm at the sudden attack and giving the player some clue as to what to do. After that, everything just becomes one big jumbled mess. My wingmen started dropping like flies, which is made all the more conspicuous by the fact that they were protected in the first mission, and the bombers didn't seem to have any real effect against the two enemy destroyers. In the end, I wound up getting killed because I was completely overwhelmed by enemy fighters.
Overall, I really like the concept that you guys have created, but whatever's going on with mission 3 is preventing me from moving forward unless I cheat my way through. I'm going to hold off on playing any further for the moment, just to see if it gets resolved.