The only issue I see with the models directly from the game files is the turrets, since we're going to need them to move. Other than that, thankfully a lot of the weapons are forward-facing, like beams and railguns.
One thing we're going to have to decide from the very start is if players of this fledgling mod will be flying strikecraft or capital ships.
Strikecraft pros:
-greater sense of epic scale, it's always awesome to watch capital ships duke it out
-more conventional space-sim experience
Strikecraft cons:
-very limited selection of ships and weapons; technically, there's one fighter and one bomber for each of the 3 races, and they only use one weapon each...but it's pretty much a given that we're gonna have to deviate from strict canon anyway, since flying a strikecraft without secondaries would be sorta boring; so, we can add more weapons and maybe even a couple more strikecraft (add some canards or extra engines or whatever onto the models)
Capital ship pros:
-Strict interpretation of canon
-C'mon, look at that Kol up there on the first page and tell me you wouldn't want to fly that

Capital ship cons:
-General lack of speed and maneuverability, might alienate a possible audience
Capital ship special abilities are also going to be interesting as we figure out how to implement them (or not, as the case may be), but thanks to the brilliant Blue Planet folks, we at least know that it may be possible for our purposes. Actually, come to think of it, almost every ship has some kind of a special ability sets it apart - a lot of them may just have to be done via SEXPs in missions, like the mission is to cover a Hoshiko as it repairs a crippled Kol while under attack from a Vasari strikeforce or something.
One more thing - does anyone know if it's possible to make secondaries that bypass shields (I know AA beams do)? Phase missiles would be fun to play with. Actually, the Vasari would have a lot of interesting stuff to mess around with. I can just imagine the awesome particle effects for wave cannons now. Maybe we can even incorporate space mines somehow - clearing minefields could be a nail-biter if done right.