Here I am again with more suggestions.
For torpedoes, you might want a way for a ship to fire say mostly single shot, but occasionally switch to a "sierra" style spread. The first, would be to use a sexp which doesn't exist right now (IIRC) but has been proposed, which would switch a turret from one type to another. If you needed a ship to fire a Sierra at a specific time, you could switch to that type, fire, then switch back afterwards with sexps. The other way, would be to have each torpedo bay actually have 2 turrets very close to each other, one mounting single shot, the other mounting Sierras. Then, give the Sierra bay a very low fire rate, on the scale of minutes, so its less of an overkill. Also, you might want to consider creating a Quantum torpedo, with a more bluish color and either a pierce flag, or a high shield dammage factor.
Another suggestion is gonna be a lot harder, and it goes much further than just adding to your Galaxy or Sovereign designs... it tries to simulate the ST style warping out. I've given this some serious thought (well, the best I could considering my abilities), and I think that most of the effects could be done.
First, unlike FS ships, ST ships usually aim in the direction they want to go before going to warp, rather than just jumping from whatever direction they happen to be aiming. This could be simulated by sexps. For example, a cap-ship engagement has taken place, and one side of say 5 ships has been outnumbered and must retreat. When the time to retreat has come, you'd use the waypoints-once command to tell your fleet to aim for a point in the direction they're retreating in. You'd have to experiment to know how long it takes all your ships to get lined up, then make the entry in the ships' editor departure cues for x seconds after the event to follow the waypoints has been true.
The second thing is probably gonna require a coder to make some changes for the conversion. Just as when you press the button to enter subspace and you hear the warmup sound, we need both a warmup and warping sound, as well as an ani file for the brightening and the flash of the warp engines. This would need to be applied only when a ship is going to warp, and happen rather quickly, say in less than .5 seconds, because of the 3rd step.
The third step is to simulate the rapid acceleration of the warping. There is likely a way to simulate this, since ships in FS already accelerate beyond their tbl-defined top speed when entering subspace. Each class of ship seems to have both a critical velocity they must reach before the warp hole appears and the ship disapears from sensors, as well as an acceleration factor... the second of which may be fixed. You'll notice that small ships enter subspace from about 50 to 75 m/s, while small cap-ships do it at about 150-200, and destroyers+ do it at more than 300. If we could change this figure to somewhere in the 1000+ or so range, it would jump out of view rather quickly. As far as acceleration to the critical velocity is concerned, it could be listed as an actual acceleration figure in M/s squared, or as a time factor, saying that it will reach critical velocity in 3 seconds. I'm also not sure, if it is the second possibility, if this time figure is the same for all classes. In any case, we need to change that figure so that it reaches critical velocity in no more than 1.5 seconds.
The fourth step simulates the post-warp flash. This would be done by replacing the warp ani with a bright flash ani, not using the warp.pof, and ensuring that the effect happens much more quickly than the current.
The effect: your ship aims at its destination, there's a bright flash from the warp nacelles accompanied by the ship shooting up to warp speed, followed by a bright flash at its departure point. The only thing we realy can't simulate is the stretching effect during acceleration. Naturally, the ani for the nacelle flash would need to be customized for each ship, or at least for each nacelle style, since Galaxy and Nebula classes share the same nacelles, same for Constitution, Miranda, Soyuz, etc.
I hope those with the means can make some use of this. Good luck!
Later!