After taking a while to play through this several times, I figured it was time to give my two cents on this:
First of all, major props to the entire dev team. You truly created the Battlestar Galactica experience so many have tried and failed to. In particular I'd like to thank those responsible for the voice acting assets, as that is what truly sold this like no other FreeSpace mod has, in my opinion, ever done. At the very first launch tube sequence, thanks to both the voice and sound assets, I had totally bought into the illusion. Masterful job guys, truly masterful.
Now for what you've all been waiting for, and what I somewhat grudgingly do: the constructive criticism. My largest gripe would have to be the role of missiles within the game, specifically anti-fighter missiles and nukes.
Firstly, the Viper's anti-fighter missiles (I forget the name at the time) are virtually ineffective at their purpose. Their flight performance is precisely what should be expected and produced in a missile (again props to the team for the flight models), but the warhead is akin to throwing a stone at a tank. If a few rounds can bring down a Raider, I would suspect a high explosive warhead detonating right against the hull would have a rather drastic and commonly fatal effect. However, every time I bother to fire a missile, I at most get ~10-30%, at the most 40%, return in hull damage on the target. With missile range so limited, its a infinitely more efficient use of my time to simply use guns and move on to the next toaster.
As for nukes, this is mainly an implementation issue. Having the nukes appear exactly the same as normal missiles visually is perfect and introduces a tenseness to the gameplay, but it is often extremely difficult to sort through the mostly harmless missile spam to find the one nuke you're hunting. I'm not sure its possible to assign them a higher priority when using the B key, but it would be appreciated.
Lastly, in the current version nukes simply aren't nukes. They're fancy heavy torpedoes. I see a nuke about to impact a ship, I expect a large flash and shockwave, and likely significant damage to the target ship. If a nuke can crack Galactica's flight pods with a direct hit, I again expect to see some damage accomplished. Instead, there's a teeny little bang, virtually no different from any other torpedo, with modestly more damage. It creates a very underwhelming melodrama that detracts from the thrill of needing to eliminate these missiles. Nukes are meant to be scary, and at the moment they simply aren't. Personally I would recommend upping the damage they do while decreasing the number fired in order to balance the tradeoff, but this is again my opinion.
I respect that I am in no means an expert, merely a humble fan, but I think it's always a good idea to throw my ideas out there. Let me reiterate on my initial words, and say that these comments are in no way a detraction from the dev team and what they've created. Shattered Armistice is, as it stands, still an amazing experience that can only get better.
(tl;dr, fighter missiles wimpy, so are nukes, awesome job guys)