Not every class of ships should get some special abilitys. I was noted, that they allready have. And we have taccruisers (Breen), sciescorts (Vesta), scicruisers (Atrox, Ambassador to some point). When i write taccruiser i don't think that it is a ship for a tac but that its role is more the one of a escorts with many things a cruiser can do.
So, it would be better to have som passive and maybe active abilitys for every single ship.
The Intrepid (and all Intrepid style ships) get subsystem disable 2 because of the gelpacks. And maybe a buff to the sensor scan.
And some disadvantage.
Sensor buff could go to the Trident too for example.
All Defaint type vessels get a special hull armor. The first direct to hull hits won't do much damage because of the special armor. But when its gone it is gone (until the next respawn or mapchange). So after some amount of dmg you will lose it and possible one of your subsystems might loose energy or fail.
One of the cruisers could get the special to redirect more energy to all subsystems but that is the reserveenergy, so after a use power on all subsystems will drop below normal for some time (possible the sovvi, i remeber Nemesis). And the ship could be more woundable to subsystem attack.
You could even make a ship hitting harder depending on shipspeed (one for fast one for slow). Or a cruiser that got a special shield desing that absorbs 10% more damage from pulse, 7,5% more from beam and 5% more damage from kinetic weapons without loosing more power then normal.
You could even combine this with the range you are fire from. Some ships are more resilent to fire from a short range while some take more damage from that.
And i would give all kling ship some base damage resistence, because they have stronger armor then feds. As a trade Feds get a little higher shieldmod.
Possible on the low level variants there are less mods and with a higher baselevel there are more.