Temporary Power-Ups?
Ships in Star Control are fun arcade space ships. They are not serious warships in space with 4 primary weapons, 8 secondaries, mines, missiles, tractor beams and transporters. A ship in Star Control has 1 or 2 weapons/devices and those systems generally launch a single projectile or missile. They are very simple, and defined mostly by the weapon/device they have. They mentioned that so far all ships have 2 systems, and that sounds promising. That's how ships in Star Control should be. However, this also means that certain weapons and devices common to the genre are too powerful for a ship to have. Systems like these could be brought into the game through temporary power-ups. This of course means more programming, art, animations, and sound for each so may not be feasible for that reason, but if it is a possiblity this could allow for some fun weapons/devices that would otherwise be too powerful to balance within these very simple ships.
Some examples of "power-ups" that must be earned in some way, and then you have it until you use it or that fight ends would be...
Gravitic Pulse - Subspace calls it "Repel". A shockwave that does no damage flings enemy ships within range away from the repelling ship.
Rocket Boosters - This might actually be possible as a balanced permenant system on a ship, but if none of the ships have them this would also make a good powerup.
Multi-fire - An extra projectile is fired for every push of the button.
You get the idea. There are things that are too powerful to balance among ships with so few capabilities and these could be put into the game as temporary power ups and would add tactical variety to the combat.