Okay, I'm currently at least a big chunk of the way through the campaign for the first time, and I'll post some more thorough and detailed feedback later. I want to bring up a few points right now, though, while it's convenient:
1) Why is Alpha wing deployed by itself so often, even when there is no realistic reason for this? It gets especially glaring when you're tasking four pilots, only moderately equipped, to escort several big/slow ships with paper-thin hull while simultaneously taking on two dozen fighters and bombers--and then take out a cruiser's main beam cannon. Stuff like this happens all the time, even when there should be at least one more wing of fighters with you, as your mission is critical, substantial hostile forces are expected, and there are a considerable amount of wings available already. Gameplay-wise, it's just not as fun; you feel all the more like you have to do everything yourself, that you have to be everywhere at once, and that you can't really strategize.
2) Please stop with the Lovecraftian names. I know that it's an artistic style (maybe even theme), so this point is probably moot anyway (as, perhaps, it should be?), but I have extreme difficulty in remembering the spelling and pronunciation of their names (this is not helped by various characters pronouncing them differently, often times pronouncing them in ways that seem to contradict the spelling), which is also a matter of realism (no military would choose unpronounceable and very difficult to spell names for enemy targets/ships on regular occasion). That, and Lovecraft, for all of the artistic genius and innovation he was, had an extremely distorted view of humanity and life in general (just look at his personal life/personality/history/health--no offense to him meant). It's probably a terrible thing for morale, too; it makes the Shivans all the more alien (in a bad way), and the effects would likely be quite significant across the board.
3) This SD Lucifer, at one briefing, was mentioned rather jarringly: it said that, according to simulations run and a plethora of scan data, if the GTVA Colossus and this Lucifer faced off, the Colossus would only have a 22% chance of victory. This goes against everything in canon, in some ways to an impossibly contradictory degree. The Colossus was designed to take on multiple Lucifer-class superdestroyers simultaneously and win. Six Lucifers can fit inside the Colossus' hull. The Colossus has 1 million hitpoints to the Lucifer's 800,000, moves at 35 m/s to the Lucifer's 15, and houses 240 craft to the Lucifer's 40-64. Its beam cannons, even if it could only bring two of them to bear on the Lucifer at once, would out-damage the Shivan vessel. Combine that with the fact that the Colossus is highly effective from all sides, while the Lucifer is comparatively toothless anywhere except in front, and the Colossus' far superior speed...yeah. The Nyarlothep-something should have little chance of victory. FS2's stats on the Lucifer are even less favorable than FS1's. If the Colossus can compromise the Nyar's shield system, then the Colossus' vastly superior fighter force can swarm and cripple the Lucifer vessel in short order. I think it's safe to assume that if even two of the five reactors on the Nyar were disabled, its shield system would no longer operate effectively--and the Colossus' beam cannons are specifically designed to be more than capable of killing a Lucifer (or more than one, simultaneously). If the Colossus overdrives its beam cannons, then the Nyar stands no chance.
4) That mission where you're supposed to protect that medical ship that jumped too close to a planet (its gravitational pull threw off its jump, and Command expects the same to happen to other ships in the area)--I coincidentally saved that other ship that jumps in (I think it's a Triton) by engaging and killing the four Dragon fighters immediately. As a result, the mission was totally broken; even fastforwarding to max, nothing further would happen. I later realized that you're ordered not to come to that ship's aid (because you had to protect the much more important and populated medical ship, and the Triton was too far away--or supposed to be), and that it's supposed to be destroyed in short order by the Dragon wing. My first playthrough, I happened to be in the area already (I accidentally lost my bearings, and wasn't closely escorting the medical ship, though my wingmates were ordered to), engaged the Dragons immediately and without thought, and didn't even realize I had done anything "wrong".