Some ideas as general rules for Star Trek Armada ships:
Leaky Shields
Whenever a ship cause 2 critical hits or more against a Star Trek ship that has either only one shield or no shields at full strength, the attacker can deal one damage card to the defender instead of allocatin the hit to a shield. A ship cannot be destroyed this way.
or already dealt damage cards are upped to cric damage.
Pointy Defense
Star Trek ships may not fire on all squadrons in a firing arc, but only on one squadron. Accuracy Results may be swapt to hit results.
Warp
Navigate Command: May perform a single, straight 5-8 Movement, but may not fire anything else than red dice that turn.