I am curious as to what you have tried in terms of your Star Trek themed ships. I can see that a purely laser strategy would have issue but if we interpret "photon torpedoes" as large long range missiles it might be possible to make something battle worthy (i. e. not get blown to pieces before firing).
I thought the theme of the Federation was really powerful sensor technology which would go well with large long range missiles. This also happens to work well with ships that aren't particularly good at taking damage.
I think the main challenge with applying designs from science fiction to Aurora is how powerful missiles are in Aurora.
My problems were twofold. Even with "photon torpedoes" you run into the problem that they always seem to be secondary to phasers (or at least equal with) so you can't really have a torpedoes only warship. (They also don't seem to be very long ranged, so perhaps a closer match would be large, very fast, minimal endurance missiles to be used for shock damage during a laser battle?)
But that pales into insignificance compared with the problem that Star Trek ships are not clearly not dedicated warships, and are stand alone not specialist. So those big sensors have to be on every ship, (along with "scientific" geological sensors really). And each ship needs its own jump drive, enough fuel and maintenance supplies for deep space operations etc etc. It soon ebcomes very expensive and very inefficient.
Totally agree about missiles. Can anyone think of a missile friendly sci-fi setting? I need something to inspire me to love them.