Sorry to steal someone's idea on the "Evil looking cruiser turret" thread, but how about making flamethrower sorts of weapon?
Give them short range (100 meter), very high refire rate (so it looks like one stream), very high energy consumption and damage. It would be a weapon of choice for 1 on 1, right?
EDIT: And logically, practically no shield damage.
EDIT: And not really a flamethrower, but a flamethrower styled weapon.
While a literal flamethrower would be pretty silly, a plasma stream would hurt... a lot... to put it lightly. I can see a gunboat or cruiser using something like that as a forward gun- perhaps a very short-range (although 100m is pretty insane, perhaps 3-500?) higher DPS weapon with a fairly quick refire rate (let's say 8-12, with a fat projectile) isn't too much to ask. I think. Although, that would first require the option of different types of forward guns- not just the one that the ship was balanced around. That could be where it runs into trouble- especially since it would only really be useful on transports, as getting that close to a smaller ship is practically impossible and getting that close to a larger one is suicide. Hmm.
Wouldn't the lag issue be reduced considerably if it's only possible to mount one on a ship? I'm thinking forward guns and torpedo mounts specifically.