I agree, the way it currently is simply doesnt make sense.
You have same range, but more chance to hit, with the mortar because its a turet and can be aimed, were the main gun can simply be pointed.
VERY useful against big ships, enemies that dont dodge. Ive took out a LOT of gunboats with it because they dont dodge. At all. I've even took out a single bomber with it, in a one in a million lucky shot on a bomber that wasnt dodging at all as I was in reverse thrust engine kill. However, the way it is simply makes the ship too weak aganst another cruiser because while the other cruiser has more guns (regular turrets) PLUS heavy turret mounted weaponry that can track a target (mortars etc).
At the very least, the cockpit of the cruiser needs a big crosshair in the center of the screen.
As for your uber damage, slow as hell approach, the problem is that if the target has a sliver of sheild power left, no hull damage will be done. Unless on impact it does damage for 2-3 second (IE: it hits, and the hit continues to deliver PAST the sheilds). That would also be acceptable, as it would make it uniquely lethal (both in balance and RP sense) while at the same time making it no more limited than it allready is.
Or, for minimal changes, since it is an energy based weapon, allow it a several degree rotation off of center, to make aiming a LITTLE more feasable (read: You still have to point, but dont have to point perfectly, you can afford to be slightly off especily at range)