That's just it, though, it NEEDS to be longer. Otherwise we have the SFC3 warp in/warp out maneuvers that made the game pretty much an arcade game. I'd also like a cool-down period for the Nacelles, where they have to be inactive, maybe for up to 5 minutes, before they can be used again safely. (You can risk it, at the expense of Nacelle Damage, just like an HET failure, although I wouldn't make it a ship wide system failure) While maybe a minute-ten is too long, I think even 30 seconds is too short. That is something will have to be play-tested to death. Another thing that I wanted to see in SFC3, I even had asked Mr. Ferrel at the time, was to make Nacelles hittable, and if they take even a little bit of damage, it greatly affects your ability to Warp. If the damage is moderate, you can't use the Nacelle at all. A big problem for 1 or 2 Nacelle Ships, 3 or 4 Nacelle Ships could try to re-balance to make up for the damaged Nacelle, but you weren't going anywhere very fast down a Nacelle.
The reasoning behind taking power from the systems is that there has to be some downside to going to Warp, most of the time you're using it to disengage, its rare that you're actually using it to maneuver around the battle zone. One other item regarding Torpedoes though. Canon has Torpedoes as physical objects that need to be reloaded, although almost every Star Trek game has them as something that simply requires power. (A Final Unity, The Rebel Universe and Bridge Commander are the only ones that comes to mind that actually kept track of how many Torpedoes the Enterprise (or the ship in general) had left.) If they are handled as physical objects here, then of course they can be available for use at Warp, since there's no power requirements outside of the power used to launch the Torpedo to begin with, which could be pulled from various sources, Aux Power, Batteries, etc.