Here is my thoughts
First off, add the Cardassians, Dominion, and Ferengi as playable races
Give the Breen ship to the Dominion
Give them Polaron Torps, Myo Beams, and Polaron Beams (Primary weapon with the damage of Phasers, rate of RomDisruptors, and 15% chance of shield penetration
Give the Cardassians KlingonDizzies, Probably Plasma, and a Plasma Wave (ESG, Voyager episode "Dreadnought')
They should also have slow speed, poor turning, bbut good hull
The Ferengi should have KDisruptors and KPhotons. In addition they should have missiles (Drones
)
They will be a lot more balanced. 6 damage (less when there is more AV), seeking, speeds 20, 40, and 60. Requires a heavy hard-point for a missile launcher. The faster load launchers require more mass. No scatterpack, but one missile per hard-point (Marauder should have 4 hard-points)
Add: Valdore, miranda, and some Klink and Borg ships.
Add: Fighters and PFs. Each level has a higher mass hold (shuttles have a mass of 1, Fighter Squadrens have 4, PFs have 8) Basic: 2 Medium: 4 Large: 8 Advanced: 12 Station: 20
Runabouts would be the Fed PF, Perrigrine would be their fighter
Roms have Scorpians and an advanced "Cloaking" Shuttle
Borg will be different
Shuttles take up lots of mass and more than a basic will slow down your ship considerably
I could think of more, but this will do