I just posted my ideas for beam/missile balance in the C# forum; this isn't really part of the actual balance part but rather a cool idea I had, so I figured it fit better here.
New weapon: Ion cannon. Works similarly to a laser, except does double the base damage with the same energy need. Does normal (which is to say, double) damage to shields, skips armor, and only rolls to hit weapons and reactors in the same way microwaves only roll to hit electronics.
If it hits a weapon, it reduces charge in that weapon on a one for one basis (1 ion cannon damage to 1 weapon charge), up to the max charge of the weapon (so if a laser has 3 out of 3 power stored, it becomes 0; if it already fired that increment and has 0 out of 3, it becomes -3 out of 3). Doesn't actually damage the weapon. If the ion cannon still has remaining damage, it rolls to hit another part.
If it hits a reactor, it makes the standard roll to damage, and (assuming a normal weapon would destroy the component) then rolls the reactor explosion chance. If it rolls an explosion, the reactor blows up, taking out the component and doing internal damage as normal. If it rolls that the reactor wouldn't explode, the component is undamaged. If the ion cannon still has remaining damage, it keeps rolling to hit other parts.
This would produce a weapon that was good against shields (a role that's kind of lacking in Aurora) and had fun effects against beam warships as well. Could maybe work on engines like it works on reactors if only damaging beam warships ends up too weak. Though that might be pretty brokenly overpowered, when you combine Laser level performance and armor piercing.
Similarly, I think it would be cool if when designing a beam weapon you could devote tonnage to additional capacitor (so that, say, a laser or railgun that needed 8 power to fire could store 24 power, then fire three times in sequential 5 second increments instead of waiting to restore back to 8 power; actual recharge rate would remain the same). Both these suggestions wouldn't mean much in the current version of Aurora but would be more useful if changes make beam combat more common.