I only like the chargeup effect for lasers, make that the effect for all of them. If you shoot in one spot determined by the ship's size (if less than 100 volume, 1 block, <500 2 by 2,<1000 3by 3, <2000 4by4, ect.)with every shot fired and within x* seconds of the last hit you would deal more and more damage and eventually (after a certain amount of concentrated fire) deal a very slight(.1-1%) shield penitration.
Certain weapons have to be faster or slower, depending on their reload time. Beams would stack as they did damage, and would only be able to stack on multible charges with cannon and regular fire(beam-pulse would deal more and more damage if it hit the same spot in one fire, but the multiplier would reset after each recharge.